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1. BLASTN Q2 50 priority m klee batch Delete jobs Delete View job results using Complete entries View Run job again with different options Edit Options Figure 1 20 Job Status page 25 26 SRS Quick Tour 3 The icon shows that the application has finished Click on the hyperlink temp blastn_ to access the results Quick Searches Help Center 2 Projects Information Apply Options to selected results only 9 unselected results only Result Options Launch analysis tool HmmBuild Launch Show tools relevant to these results Tools Link to related information Link Save Display Options View results using Save results Complete entries v Show 30 results per page Printer friendly view C Apply Display Options Query BLASTN JobName temp job1 found 50 entries next BLASTN temp jobi emblnew 1 AY069346 emb AY069346 AY069346 Drosophila melanogaster LD05574 full length cDNA Length 2285 Score 61 9 bits 31 Expect 4e 08 Identities 58 67 865 Strand Plus Plus Query 155 ggcactgcccgttatgcctccatcaacacgcatctcggecgtcgagcagtctegccgtgac 214 FELLEEEEEEEE FEEEELEEE Tedd T Ted FEE Tadd F1 1 GF gl Sbjct 999 ggcactgcccgctatgcctcgatcaatgcccatctgggcatcgagcagtcgcegagcgtgac 1058 Query 215 gacatgg 221 EET FN LG I Sbjct 1059 gacatgg 1065 Score 54 0 bits 27 Expect 1e 05 Identities
2. 0 0 100 0 200 0 300 0 400 0 gt SWISSPROT 2NPD WILMR 2 nitropropane 100 0 dioxygenase EC 1 13 11 32 90 0 Nitroalkane oxidase 2 NPD 80 0 70 0 60 0 50 0 40 0 t 0 0 100 0 200 0 300 0 400 0 SWISSPROT ACC3 LYCES jie 100 0 aminocyclopropane 1 carboxylate 90 0 E oxidase homolog Protein E8 80 0 70 0 60 0 50 0 40 0 pe 0 0 100 0 200 0 300 0 400 0 Figure 5 4 The Query Result page using the selected view From the Query Result Page Querying linking and launching applications always returns the Query Result page This page contains a list of the LION Bioscience entries that meet the requirements specified in your query If you do not select a view for the results when the operation is run a default view is used To change the view on the Query Result page In the Display Options box you will see a drop down list below the text View results using see Figure 5 5 The drop down list displays the name of the view currently applied 115 Views 9 LION uick A Select Databanks Help Center O Results Projects ustom Information C selected results only unselected results only Result Options Launch analysis tool Blast Launch Show tools relevant to these results Tools Link to related information Link Save results Save Display Options View results using prateinChart Names only
3. Figure 3 21 Query Result page showing the results from a search of the SWISS PROT Description field for the word kinase 2 Choose the Organism Name field from the Sort Results by drop down list 83 84 Querying with SRS Display Options View results using SeqsimpleView pe Sort results by unsorted g unsorted Primary Accession Number Description Gene Name Entry Creation Date Organism Name Organelle Sequence Length Apply Display Options Figure 3 22 Display Options area showing drop down list of available sort fields Note Entries for which the chosen sort field is missing or null will be listed at the bottom of a sorted list whether sorting was in ascending or descending order 3 For this example choose to sort in an ascending order Note Unsorted results will be listed in ascending order It is not possible to reverse this order for unsorted results 4 You might also like to apply a different view to the results perhaps one that shows the field on which you are sorting For this example choose SwissView LION Bioscience Display Options View results using SwissView Sort results by Organism Name ascending C descending Show 30 x results per page Printer friendly view T Apply Display Options Figure 3 23 Choose the order for sorting and a view to display the results 5 Initiate sorting by clicking on the _Apply Display Options button The r
4. Mar z 2002 9 Mar 2003 m LastUpdated seet Hh A an A M 1 A an A fr r Sequence Length pae ex e r References Iib Search References subentry fields View results using Figure 3 1 Extended Query Form showing a numerical data query being set up using the drop down lists See chapter 8 SRS Query Language p 155 for more details on the syntax for numerical searches 3 1 4 Regular Expressions 3 1 5 Wildcards Regular expression searches are useful when you wish to search for alternative spellings or words with the same root but different suffixes etc Regular expressions allow you to use a combination of characters along with regular expression characters and get a list of matching entries as your result You always need to include the forward slash character at the start and end of the regular expression string For example phos will find all words beginning with phos e g phosphate phosphorylase ase will find words ending in ase e g kinase phosphatase See section Regular Expressions p 159 for an explanation The SRS query language also uses the familiar and wildcards This is usually much simpler than using regular 59 Querying with SRS expressions for basic searches For example cell ase would find all words starting with cell and ending in ase e g cellobiase cellobiohydrolase cell
5. A databank entry may contain references to other databanks and vice versa In SRS these relationships are known as links and can be used to extend a query across multiple databanks Thus you can obtain all the entries in one databank that are linked to an entry or entries in another databank From a user perspective there are two types of link hypertext links and index links query links Hypertext links are links between entries which are displayed as hypertext These are hardcoded into SRS and you can use them whenever you wish They are useful for examining entries that are referenced directly from entries Index links are built into the SRS indices at the same time as databanks are added They allow you to construct queries using relationships between databanks They require SRS to search through entries or indices in other databanks looking for matches It is assumed that you are already familiar with hypertext links so only a limited demonstration of them is given in this chapter see section 4 2 Hypertext Links p 92 The remainder of this chapter is devoted to explaining index links 4 2 Hypertext Links Some entries have hypertext links which allow you to access linked entries directly Example 4 1 shows such an entry LION Bioscience Example 4 1 Accessing a hypertext linked entry 1 Query EMBL for entries whose description field contains the word kinase EMBL entries will be displayed on the Query Re
6. Journal YolumeNo FirstPage Year MedlineID PubMedID RefPosition RefcommentCode M RefComment Fields of subentry Comment CommentType Comment Fields of subentry Feature Ftkey FtLength FtDescription Fields of subentry Counter CountedItem CountedN EMBL F ID Division AccNumber M PrimAccNumber Seqversion M Molecule M Description Keywords Organism D Taxon Organelle Comment DateCreated LastUpdated SegLength J Link r Sequence festa x Fields of subentry References D ID Authors Title Journal volumeNo P FirstPage Year MedlineID PubMedID X RefPosition Fields of subentry Features F ID AccNumber M FtKey FtQualifier ProteinID Gene FtDescription FtLength n Sequence gcg z Fields of subentry Counters F ID CountedItem CountedN Use explicit link D Use view to display entries nne s Display only number of linked entries only OD m Save New View Figure 5 22 Select the datafields to be included in your view LION Bioscience Note Each field name is a hypertext link to its Field Informa tion page see section on the Information Pages Field Infor mation in the Online Help So if you want to know more about a particular field use these hypertext links to find out 9 Click on the Save button Your new view can now be used for any of the databanks indicated in the root
7. Results Projects LION Bioscience Help Center O Information Query BLASTN JobName temp_job1 found 17 entries Apply Options to BLASTN Query Search Database BLASTN temp jobi e 40104140 BLASTN emb new 2 AX305845 BLASTN temp jobi temp jobi emb new AP001551 B LASTN itemp jobi emb new AxX305600 B LASTN temp jobi emb new AF443205 LASTN emb new SPBCSD2 LASTN temp jobi temp jobi emb new AY069346 LASTN temp jobi emb new 8 4 064020 LASTN temp jobi emb new ACO23741 LASTN emb new i0 ACO23681 LASTN temp jobi temp jobi emb new 11 NC18F11 LASTN temp jobi emb new 12 CEFO7AS B LASTN temp jobi emb new 13 4 069602 B LASTN temp jobi emb new 14 AYO053423 BLASTN temp jobi emblnew 15 AP003407 BLASTN temp jobi emblnew 16 AL646060 BLASTN temp jobi emblnew 17 ACO091221 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 EMBL 44901632 emb emb emb emb emb emb emb emb emb emb emb emb emb emb emb emb new
8. new new new new new new new new new new new new new new new Figure 6 7 Entry page showing open Ba Alternatively it is possible to select a job by ticking the check box beside it selecting a view and clicking the ie button zemb ACi04140 AC104140 zemb AxX305845 Ax305845 zemb APO001551 APOO1551 zemb Ax305600 A x305600 zemb AF443205 AF443205 gt emb 4L022072 SPBC8D2 zemb Av0659346 AY069346 zemb AYv054020 AY064020 zemb AC023741 AC023741 zemb AC023681 AC023681 zemb AL670011 NC18F11 zemb z72506 CEF07A5 zemb Av O69602 AY069502 zemb Av053423 AY053423 gt emb 4P003407 4P003407 zemb AL646060 AL646060 zemb ACO091221 AC091221 This will display the results on a Query Result page 6 4 3 4 Job Status The Job Status page see Figure 6 8 lists all batch jobs in 145 146 Analysis Tools the current project and shows their current status The most recent job is at the top of the list e Completed jobs are shown with a icon Jobs still running are shown with a zX icon e Waiting jobs i e those which are waiting to be run are shown with a 5 icon Jobs that have been submitted to the queue are shown with aa R icon e Jobs which have produced no meaningful results e g those for which the search sequence produced no appropri ate results or those which have crashed are shown with a X icon e Jobs whic
9. put an exclamation mark in front of it The absence of a number on the left indicates that the search should start at the minimum value in the index Similarly an absent value on the right indicates that the search should include values up to the maximum for that index Table 8 3 Examples of queries on an index of the sequence length Written Range Meaning 400 All sequences with a length of exactly 400 400 500 All sequences with lengths between 400 and 500 400 All sequences with lengths greater than 400 500 All sequences with lengths less than 500 400 500 All sequences with lengths between 400 and 500 excluding 500 A range from the minimum value to the max imum value i e all sequences LION Bioscience 163 Combining Ranges Ranges can be combined using logical operators For instance either 300 1500 600 700 or 300 700 500 600 would retrieve the same set of sequences i e all sequences from 300 to 500 excluding 500 and all sequences from 600 to 700 excluding 600 8 2 5 Searching for Dates Searches for dates can be made using one of the two special formats recognized by the SRS query language These are YYYYMMDD or DD MMM YYY Y For example 20020619 19 Jun 2002 Dates can be used within ranges in the same way as other numbers For example swissprot date 20010415 20020414 swissprot date 15 APR 2001 14 APR 2002 164 SRS Query Language 8 2 6 Searching Multi
10. 1 SwISSPROT AMY BACAM Alpha amylase precursor EC 3 2 1 1 1 4 alpha Show 30 MI results P00692 D glucan glucanohydrolase 2E per page SWISSPROT AMY BACCI Alpha amylase precursor EC 3 2 1 1 1 4 alpha rug AMI Baugi P08137 D glucan glucanohydrolase 528 Printer friendly view CI SWISSPROT AMY BACME popg4s Alpha amylase precursor EC 3 2 1 1 1 4 alpha 520 ye iN Sg sas D glucan glucanohydrolase Apply Display Options SWISSPROT AMY BACST ppe279 Alpha amylase precursor EC 3 2 1 1 1 4 alpha 549 Di nliic2n alieanahwdralacal Figure 5 15 Query Result page showing a table view Select LION Bioscience Help Center 2 Quick Searches SRS Reset Apply Options to selected results only 9 unselected results only Result Options Launch analysis tool BlestP v Launch Show tools relevant to these results Tools Link to related information Link Save results Save Display Options View results using SWISSPROT v Sort results by unsorted Y 9 ascending descending Show 30 per page results Printer friendly view C Apply Display Options Databanks Query swissprot AllText amylase found 99 entries Results Projects Information next SWISSPROT AM3D ORYSA P27933 Alpha amylase isozyme glucanohydrolase AMY1 3 OR AMY3D 01 AUG 1992 Rel 23 01 AUG 1992 Rel 23 15 DEC 1998 Rel 37 SWISSPROT AM
11. 42 47 89 Strand Plus Plus Query 3 ttcatccaccgcgacatcaagcctgacaacttccttatggggattgg 49 ELEELELEE EELEEEELEEEEEEE FEE Teter CALIL treet Sbjct 846 ttcatccatcgcgacatcaagccggataacttcctaatgggcattgg 892 O BLASTN temp jobi emblnew 2 AKO004606 emb AK004606 AK004606 Mus musculus adult male lung cDNA RIKEN Figure 1 21 Entry page showing the application results 1 7 2 Running an Interactive Tool LION Bioscience 9 LION Quick Searches Reset Result Display Options View results using Blast View A Shaw 30 M results per page Show results automatically v Parameter set options Save current parameter set as Select Query Databanks Strand of query sequence to use Both _ Codon Trans 1 If your tool is not run via a batch queueing system i e it is run interactively then the Launch page should look some thing like that shown in Figure 1 22 Help Center O pad Tools Results f Projects Custom Views Information BlastX More Info Job name Database to search ENT Launch unc temp SWISSPROT Updates eu EMBL MMNKX begin 1 1 11 21 31 41 51 egaggggecaggtacaggggcaggeagggectgagetctgtagaggaggtactcgggggt 61 101 111 d gtgtcagagcagcacaggtcaccagagcttcetgagcaaaaagaggagacctcaagactat enc 1972 121 131 141 151 161 171 etteccattggcecaagagagaaagetttcaggg acaggcaagaggaggagggcaccgag v lt ti ation table Standard Genetic Code v Output Options Search Par
12. Apply Display Options BLASTX temp jobi swissnew 9 HMBP DROME EMBL MMNKX swissnew gt sp P22809 HMBP DROME Figure 1 25 Query Result page showing the tool results 1 7 3 Viewing Tool Results 1 SRS provides many ways to view tool results 2 Using the drop down list below the ie button select BlastAlignment If this option is not available choose another view type noting that the figures presented below LION Bioscience 31 may refer to BlastAlignment and were generated for the BlastN results created above 3 Click the Yie button This displays the results of the tool using the BlastAlignment view See Figure 1 26 BLASTX SeqLength BLASTX temp jobl swissnew 1 HMx STRPU 162 Frame 42 a Homer 405 protein SpHmx Query 1262 ESPEKKPACRKKKTRTVFSRSQVFOLESTFDMKRYLSSSERAGLAASLHLTETQVKIWFQ 1441 H6 like SP KK KKKTRTVFSRSQVFQLESTF KRYLSSSERAGLAAFLHLTETQVKIWFQ Fragment Sbjct 247 QSPOKK KKKTRTVFSRSQVFOLESTFEVKRYLSSSERAGLAANLHLTETQVKIUFQ 302 Query 1442 NRRNKWKRQLAAELEAANLSHAA AQRIVRVPILYHENSAAE 1564 NRENKUKRO AAELE ANL HAR AQR VRVPILYHEN Sbjct 303 NRRNKUKROMAAELESANLAHAAQIRAQANLAQVSAVHVHAYAQRMVRVPILYHENHPTT 362 BLASTX temp job1 swissnew 2 HK32 MOUSE 101 Frame 42 Homeobox 333 protein NKX 3 2 Bagpipe Query 1037 DSSPASGTDR DSPEPLLKADPD HKELDSKSPDEIILEESDSEEGKKEGEAV 1189 homeobox D ASGTR DP L D E 48 E s E HV protein Sb
13. queries There are two ways to find links for your queries from the Manage your Query Results page The first and most common method is to tick the check box that corresponds to a query set and click the tisk button 100 Links to Additional Data Po LION Help Center 2 Select Query Custom Quick x Searches Databanks Form Tools Results Projects Views Information SRS Reset Search using a query expression Results Options m Search Options are applied to selected queries only Result History Save results Save Name Type Total No From No Query Expression Comment Delete results Delete Qg select 1 EME 1 EMBL ID 21640 Combine queries select 1 EMB 1 amp AND Q7 EMBL ID A21640 with be Combine Q6 select 1 EMBL 1 EHBL ID A21640 Find related info Link Qs query 1 EMBL 1 emb l ALLTEXT a21640 lt gt Results Display Options Q4 query 73271 EMBL 73441 embl Description ki View results using gt Complete entries v Q3 query 50 BLASTX 50 BLASTX JobName temp lt gt Show 30 v T results per page Q2 workflow 3 EMBL 3 EMBL alltext rumnkx lt lt gt Rerun Query Qi workflow 586050 EMBL 586050 rrmpL alltext kinase ie Figure 4 8 The Manage your Query Results page This takes you to the Link page see section 4 3 Index Links p 95 from where you can complete your search for linked data The second
14. set types Consider the two queries 174 SRS Query Language 8 4 1 Links with Sets swissprot keywords transmembrane swissprot ftkey transmem The first query retrieves all SWISS PROT entries that include transmembrane in the keywords index The ftkey index however has a special type allowing it to find features of a given type within entries Thus the second query retrieves a set of subentries within SWISS PROT entries Each subentry is a transmembrane feature Note The second query above will retrieve many more entries than the first because most transmembrane proteins have more than one membrane spanning segment If you requested the sequences for the entries in the second set you would get the transmembrane segments rather than the parent entry s sequence Containing Subentries Simple Links It is not possible to combine sets of entries with sets of subentries using the logical operators however link operators may be used between sets of entries and sets of subentries For example swissprot org human swissprot ftkey transmem returns a set of transmembrane segment subentries found in human proteins whereas swissprot org human swissprot ftkey transmem LION Bioscience returns all human proteins that have transmembrane segments Parent Links Sometimes it is necessary to do an explicit conversion from subentries to entries This can be done using the operand parent This method l
15. start new projects and swap to any other project currently on your account The Project Manager page is described in section 2 4 Using the Project Manager p 47 LION Bioscience 47 Help Center 9 LION BOING a query Tools Results Projects roar Information SRS Reset Contents of project Queries Name Query Expression Name Account Name helenp Session project1 M Qa swissprot AllText alcohol amp EFI swissprot AllText dehydrogenase rojecti Options PEG p FP Q2 swissprot AllText dehydrogenase F Q1 swissprot AllText alcohol Embl View Save to desktop Save Rename project project Rename Delete project Delete Other Projects Create a project New Project Open from desktop Browse Open Switch projects project Switch Figure 2 6 SRS Project Manager page for permanent projects 2 4 Using the Project Manager The Project Manager page is used for project administration From this page you can create a new project switch to another project copy information between projects open saved projects save projects rename projects and delete projects 48 SRS Projects These functions are described below Note Some functions namely creating a new project switch ing to other projects deleting and renaming projects are not available for temporary projects 2 4 1 Creating a New Project The Project Manager page allows you to create ne
16. subentries 173 linking 174 switch projects 48 syntax index search 157 T table view 124 125 128 temporary projects 38 41 managing 42 starting 41 tools interactive 28 141 tools See analysis tools U UNIX 150 upload 52 usernames spaces 44 special characters 44 using analysis tools 138 getz 151 LION Bioscience operators 171 views 110 V view list view 124 125 128 table view 124 125 128 view manager page 1 14 view manager page 2 15 views 109 applying 30 111 creating 123 using 110 W what are analysis tools tools 138 what is linking 92 query language 156 view 110 white spaces databank group names 164 filenames 35 51 53 131 passwords 44 usernames 44 wildcards 59 59 59 query language 159 word multiple word search terms 57 single word search terms 56 181 182
17. 1 Next Entry Entry Information Goto General Description References Comments Links Sequence Entry from General Information about the Entry Entry name SWISSPROT AI1M YEAST Prim accession P03875 Created Release 1 21 JUL 1986 Last sequence update Release 1 21 JUL 1986 Last annotation update Release 35 1 NOV 1997 Entry Options Description and Origin of the Protein Launch analysis tool BlastP v Launch Link to related information Link Save entry Save View Printer Friendly Keywords Mitochondrion Description cox1 oxi3 intron 1 protein Gene name s ail Organism source Saccharomyces cerevisiae Baker s yeast Organism classification Eukaryota Fungi Ascomycota Saccharomycotina Saccharomycetes Saccharomycetales Saccharomycetaceae Saccharomyces NCBI Taxonomy ID 4932 Organelle Mitochondrion References 1 Bonitz S G Coruzzi G Thalenfeld B E Tzagoloff A Macino G Assembly of the mitochondrial membrane system Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase J Biol Chem 255 11927 1980 Medline 81069885 PubMed 6254986 Position sequence from n a Comment strain d273 10b 2 de Zamaroczy M Bernardi G The primary structure of the mitochondrial genome of Saccharomyces cerevisiae a review Gene 47 155 1986 Medline 87163488 PubMed 3549452 Position sequence from n a Figure 5 7 Entry page using SwissEntry fo
18. 11941 1980 2 SEQUENCE FROM N MEDLINE 87163488 PubMed 3549452 de Zamaroczy M Bernardi G The primary structure of the mitochondrial genome of Saccharomyces cerevisiae a review Gene 47 155 177 1986 MISCELLANEOUS THIS PROTEIN IS CODED IN GROUP II INTRON 1 OF OXI3 COX1 SIMILARITY TO GROUP II INTRON MATURASES Figure 5 8 Entry page using Text Entry format Applying a View From the Manage your Query Results Page To apply a view from the Manage your Query Results page 1 Select the query to which you want to apply the view by ticking the check box beside it Note Only one query can be displayed at a time If more than one query is chosen only one will be displayed LION Quick Searches Reset Results Options Options are applied to selected queries only Save results Save Delete results Delete Combine queries with a AND gt Combine Find related info Link Results Display Options View results using SeqSimpleView z default view Names only Complete entries SeqSimpleview FastaSeqs DWI lew proteinChart LION Bioscience 2 Select the required view from the drop down list in the options area see Figure 5 9 Select Query Databanks Form zonis Search using a query expression Results Help Center O Custom Projects Views Information on m _ Search Result History Name Type Total No From Tr Q8
19. 2 HK32 MOUSE EMBL MMNKX swissnew gt sp P97503 HK32_ MOUSE Launch analysis tool BlestP v Launch Show tools relevant to these BLASTX temp jobi swissnew 3 HK32 HUMAN EMBL MMNKX swissnew sp P78367 HK32 HUMAN results Tools Link to related information Link NEUEN cate BLASTX temp jobi swissnew 4 HM1D DROAN EMBL MMNKX swissnew gt sp P22544 HM1D DROAN BLASTX temp jobi swissnew 5 HMX2 COTJA EMBL MMNKX swissnew sp P23410 HMX2 COTJA Display Options View results using Blast View 3 BLASTX temp jobi swissnew 6 NK2E XENLA EMBL MMNKX swissnew sp P42583 NK2E XENLA BLASTX temp jobi swissnew 7 HMX2 CHICK EMBL MMNKX swissnew sp P28362 HMX2 CHICK Show 30 E M results per page BLASTX temp jobi swissnew 8 SAX1 MOUSE EMBL MMNKX swissnew sp P42580 SAX1 MOUSE Printer friendly view C Apply Display Options BLASTX temp jobi swissnew 9 HMBP DROME EMBL MMNKX swissnew sp P22809 HMBP DROME Figure 6 3 Query Result page showing the results of an analysis using BLASTX 6 4 3 Batch Tools 6 4 3 1 Introduction to Batch Tools Tools which are likely to take a while to run are usually set to run as batch jobs SRS does not wait while batch jobs are run LION Bioscience Instead you can carry on with further queries etc and return to look at the results of your analysis when it is complete If a job will be run from the batch que
20. EMBL ISTNSO C selected results only EMBL TT903A2 unselected results only EMBL TT903A3 EMBL PRTSG 1 6 Using Views See Views Chapter 5 for more information LION Bioscience Figure 1 9 Query Result page showing the EMBL entries that had links to the SWISS PROT entry SWISSPROT ISPE_ZYMMO Accession number Q9X3W5 from the above query for kinase If there are no items linked to your selection then go back to the original Query Result page choose a different selection and try again If you want to search all your results for links to EMBL from a Query Result page click the unselected results only option in the Apply Options to area ensure that the check box beside each of the entries is unticked and repeat the search Apply Options to C selected results only unselected results only Figure 1 10 Apply Options to box Similarly by ticking several entries in your list you can search all those you have selected or all those that are not selected using the option buttons Note Searching a large number of results for links might take some time when large databanks are involved SRS allows you to customize the way in which you display data This is usually done using the View Manager pages although simple view creation is also possible from both of the 13 14 SRS Quick Tour Query Forms see section 5 3 1 Creating Views from the Query Forms p 124 1 6 1 Creating a View This ex
21. Extended Query Form results per page Figure 3 5 Standard Query Form showing a query for EMBL for entries with the keyword kinase that were added to the databank after January 1 2002 Note lf you want to know more about any of the fields choose that field from the drop down list and click the beside it 3 3 3 Using the Extended Query Form The Extended Query Form lists all the common datafields and allows you to enter search terms for as many of these fields as you want 65 Querying with SRS SRS Reset search EMBL Search Options Fields you can search Your search terms Create a view In a single field you can separate multiple values by amp m _ Search Combine search terms AllText with amp AND x ID m est fun gss hte htg hum Use wildcards M Get results of type ut l inv mam mus F org F pha F pln Entry x Division r O pro rod sts syn F unc O vyr Result Display Options Dovwt Accession Number m View results using Primary Accession Number r SegSimpleView x EE SeqVersion Im C Create a table circular dna circular rna view using selected fields Molecule M dna F rna i Sequence Format xxx embi zl Description shaw 30 Keywords results per page Organism Name Taxon E Organelle You can also use the Standard Query Form Comment Entry Creation Date select z 1 j Jan v vvvv 1 gt Jan gt head LastUpdat
22. RAT 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type II 3Beta HSD II Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase EMBL RNSBHSDB EMBL 563167 Figure 1 14 Query Result page showing typical SWISS PROT entries and any linked EMBL entries shown using myTestView If you cannot see any entries with links try looking for the entry for which you found the original link If you had to try 19 20 SRS Quick Tour linking to a databank other than EMBL you may want to create a view that will show SWISS PROT and your chosen databank rather than SWISS PROT and EMBL Do not worry at this stage if you cannot find your result 1 6 3 Deleting a View If you no longer need a view you can delete it 1 From the View Manager page 1 use the Custom Views tab to get there select the view you want to delete e g myTestView Delete View ARGNA _Delete View Figure 1 15 Selecting a view to delete 2 Click the Belete View button 1 7 Using Analysis Tools See Analysis Tools SRS is able to analyze the results of your search using many Chapter 6 for more bioinformatics analysis tools or applications This enables you inforinaulen to seek out further information that may be relevant to your initial search Thi
23. SRS Projects 2 2 2 Managing Temporary Projects LION Sree SRS If you click the Projects tab on the navigation bar the Project Manager page will be displayed see Figure 2 3 Help Center O SRS Project Options Contents of your temporary project Save to desktop Save Open from desktop Browse Open prnsectas query Tools Results Projects Scar Information Name Query Expression Name swissprot Organism homo amp swissprot Embl View Organism sapiens swissprot Swi Y vi 7 Organism homo sapiens amp swissprot wiss View Q Description kinase amp swissprot Swiss Embl View Description inhibitor swissprot Description kinase inhibitor Q6 libs embl swissprot Organism toad Q5 swissprot ID rat Q4 swissprot Description cellulase Q3 embl Description cellulase Q2 embl Description kinase Q1 swissprot AllText cyclase Figure 2 3 Project Manager for temporary projects The Project Manager page provides you with the necessary tools to manage your SRS projects Here you can save projects and open previously saved projects After completing your project you may want to save your work to disk The next time you access SRS unsaved temporary project work is unlikely to be available from the server Saving is also useful for moving temporary work to your permanent project history list or permanent project work to a temporary project or if you want to sh
24. SWISS PROT databank you would type Q3 lt SWISSPROT a z Typical operators allow you to combine searches using the standard logical functions amp AND OR BUT NOT and to look for links between result sets For more help on linking using expressions see section 4 5 Expression Linking p 104 See Table 8 5 page 168 for a list of the SRS query language operators that may be used This method of searching is very powerful because many detailed queries can be created using the SRS Query Language See chapter 8 SRS Query Language p 155 for more information LION Bioscience Using Expression Queries to Search Subentries You can use Expression Queries to search for subentries This requires a knowledge of the correct SRS query language However until you are confident enough to create your own queries you can find out the correct query syntax by looking back at the Query Result page that you have previously generated For example use the text generated in Searching for Entries which Reference Papers that are Co authored by Smith amp Jones using the Standard Query Form p 72 1 Search using a query expression suissprot Authors smith amp swi From the Select Databanks To Search page select a databank to search e g SWISS PROT Click the Results tab to display the Manage your Query Results page Enter the following text in the Expression Query text box Swissprot Aut
25. Searches using a Query Expression 000 eee ee 79 Using Expression Queries coo v es REN em a ooo EVE 80 3 6 Sorting RSS cues seras oe etae perd Fed NI Ped 82 Mila is SOT oed new Dnm hr be paste PES ed 82 Sorting a Set of Resulls soo nnu QUSS aac Tod ln S e Ae 82 3 7 Browse Index qu eto Pax e acce o po PX S ERU ud oda d 86 About Browsing Indices 0 0 0 0 cece eee 86 Browsing Indices ziii Rr 4p Y E64 RA Xd RYE 86 Getting to the Field Information Page 88 CHAPTER 4 LINKS TO ADDITIONAL DATA 0 cc cece ccc hh hh hh nn 91 4 Whatisa Link uuu necne sp peas tee oe eee Ba ades 92 47 Hypertext LINKS 5 0 see eese EVER Tee ee ES xn 92 T3 Index AMES is id a e P ae hw EA E A E ER eds 95 Searching for Data using Index Links 95 TAME ODDS eee DUE RE onn xA Cut EWR ase c Ae 98 4 4 Getting to the Link Pages osos ear nde T Rte Go 8 en 99 Finding Links from the Manage your Query Results Page 99 Finding Links from the Query Result Page 101 Finding Links from the Entry Page 4 103 45 Expression Linking iis aco tania weer ses ee ow esas ee PRESE 104 Expression Linking Procedure 5 22 ex Ver SERIA 104 Danie Operators uo ocu ta e Sleeve ad eL E 105 Expression Linking Examples 0000 107 CHAPTER 5 VIEWS oes svxe e reRERSE ORG ER SENE EERNEFRRNEESEA ERE ER wee RENS NR 109 34 Wha tis a VIEW E sar ead poe dac au
26. Sorting Results sai aet PES Oe ER pa etd 10 LAUDES S ruo ous pU ee ett Sa dead p s A arde n TO Du ipi a ra en 11 Linking to Related Information 000 11 Using VIGWS srine eho aad es Lae wee RP eed 13 Creating a VieW i c63 sansa iw ek pe REE bea be bx RE DURER 14 Applying a VIEW 2 24 240 Hota eae eatin dede ees ovale ny 17 Deleting d Views uve e vente dee cies ee E AEE E 20 Using Analysis 100ls X 4t eye ER ER ea GW SES EE 20 Running a Batch Queued Tool 0 0 0 eee eee 24 Running an Interactive Tool 0 0 0 ee eee eee 27 Viewing Tool Results 555245222 e aoe Ed SES as 30 Saving your Results 22d e kb ERES BR ROPEETARGS 31 REViOW 2 24 b228b Hada hed eraon kA eL AE eRRbbiad s A443 ess 35 a A E E a T EE E T T E 37 Introducing Projects i ueio d se inURE RIED p E TDCEEAS 38 Temporary Projects s csv ERR ex4ek xe pee de actin 38 Permanent Projects i oec ux eX Ye Rieder ex TN ERG 38 Starting a Project saa veto eX WERE None SWE NOE 39 2 2 Temporary Projects so de eae ees Ly eee Baa ae aa 41 Starting a Temporary Project 0 0 0 cee eee eee 41 Managing Temporary Projects 0 00 c eee eee eee 42 2 3 Permanent Projects ce consc a ERI EN MEREX E EX ME 43 Starting a Permanent Project 44 Managing Permanent Projects 0 0 0 0 eee eee 46 2 4 Using the Project Manager o2 22s sta c4 hee v see ds 47 Creating a New Project i iiio ra e ERE EERLAGG 48 Switching t
27. at any time This will take you to the information relevant for the page you were using when you pressed TIRNO 1 2 Starting an SRS Project See SRS Projects 1 When you access SRS the Start page is usually shown te for more first From here you can start a permanent project do a information quick search if you have the relevant databanks installed on your installation or access the online help files Note Your SRS Administrator should be able to give you the web address of your local server or of an external site to which you have access LION Bioscience P LION Help Center O Quick Select Query Custom Searches Databanks Form Tools Results Projects Views Information SRS Start a Permanent Project Quick Text Search Search Tips Want to know more about Searches Databanks EMBL m Search using SRS go to the Help Center where you ll find all the Sequence Similarity Homology Search 1 Search Tips searchable online help you need Get Protein Sequences v Problems with SRS please email the SRS administrator Searches Databanks Swissprot m _Search SRS Release 7 1 Copyright 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 1 1 The Start page Note This page is almost identical to the SRS Quick Search page that will be introduced shortly The main difference is that where the Start page has a link to allow you to start a per manent project the S
28. databanks see step 5 above Try your new view for a query on one or more of the root databanks 135 136 Views CHAPTER ANALYSIS TOOLS Various analysis tools can be run on queries within SRS This chapter describes how to Use the tools that are available within SRS 138 Analysis Tools 6 1 Introducing Analysis Tools SRS analyis tools are bioinformatics programs that use a databank query as input The output file from an analysis tool is indexed in the same way as any other databank This enables users to store and query their analyses The results from one analysis tool can be used by another Hits in a sequence databank from a sequence similarity search e g one of the BLAST programs can be selected and aligned The resulting alignment can then be used for further analysis 6 2 Accessing Analysis Tools Analyses using tools usually start with a databank query although it is possible to use sequences from other sources The Query Result page includes a Launch analysis tool drop down list that lists the most commonly used available tools This can be used to access the analysis tools in the drop down list Select a tool from the drop down list and click the Launch button Alternatively the eels button will take you to the Tool Select page This lists all the tools that can use the current query data as input You can also get to the Tool Select page by clicking on the Tools tab This will list all of
29. entries and click on its hyperlink to display the Entry page for that entry Note that you can usually view such a page using Text Entry format or in a databank specific format e g SwissEntry format LION Reset Entry Information Quick Searches Select Databanks Form Help Center O Query i Custom i Tools Results Projects Views Information Text Entry EmblEntry Entry from EMBL Entry Options Launch analysis tool BlastN v Launch Link to related information Link Save entry Save View Printer Friendly Entry 1 of 586050 from Query 9 _Next Entry 42901535 standard RNA EST 347 BP 42901535 901535 1 15 APR 1998 Rel 55 Created 11 JAN 2001 Rel 66 Last updated Version 4 NCMSB1T3 Mycelial Neurospora crassa cDNA clone NMSB1 5 end mRNA sequence EST Neurospora crassa Eukaryota Fungi Ascomycota Pezizomycotina Sordariomycetes Sordariales Sordariaceae Neurospora 1 1 347 MEDLINE 97435549 Nelson M A Kang 5 Braun E L Crawford M E Dolan P L Leonard P M Mitchell J Armijo M Bean L Blueyes E Cushing T Errett Fleharty M Gorman M Judson K Miller R Ortega J Pavlova I Perea J Todisco S Trujillo R Valentine J Wells A Werner Washburne M Yazzie 5 Natvig D 0 Expressed sequences from conidial mycelial and sexual stages of Neurospora crassa Fungal Genet Biol 21 348 363 1997 Figure 4 10 A typical En
30. entries next Figure 8 1 Query Result page showing a query of the AllText field of the SWISS PROT databank for cyclase In addition to simple searches of single databanks you can search multiple databanks link searches etc LION Bioscience 8 2 Searching in Indices 8 2 1 8 2 2 General Syntax Introduction Probably the simplest form of the SRS query language syntax is that used for simple searches in indices Index searches include searches for simple strings searches for numbers and ranges of numbers as well as searches for dates This section covers the various forms of index search An index search must specify within square brackets the databank or databank group name the index or index group name and a search expression The two names must be separated by a hyphen and be separated from the search expression by either a colon string search see section 8 2 3 Search Strings p 158 or a hash range search Range searches can be performed only in indices of the types num and real see section 8 2 4 Searching Using Numerical Ranges p 161 and section 8 2 5 Searching for Dates p 163 Either the field name e g escription or its abbreviation des can be used as the index name All strings including the search words are case insensitive For example pir des elastase 157 158 SRS Query Language 8 2 3 Search Strings searches for the string elastase in
31. entries to allow you to search for information such as dates or entries with a specified length Numerical entries can be combined into expressions using various operators This allows you to search within particular ranges Typically these operators are less than less than or equal greater than and greater than or equal These are created by combining two simpler operators namely the Querying with SRS colon and the exclamation mark The colon means greater than or less than depending on which side of your number it lies The exclamation mark indicates that the number to the right of the exclamation mark is to be excluded The exclamation mark can be regarded as not or not equal to It is probably easier to demonstrate this with some examples 12 15 Greater than or equal to 12 but less than or equal to 15 12 Greater than or equal to 12 with no specific upper limit 112 Greater than but not equal to 12 with no specific upper limit 712 Less than or equal to 12 with no specific lower limit 112 Less than but not equal to 12 with no specific lower limit When using the Extended Query Form see section 3 3 3 Using the Extended Query Form p 65 such a range search is often simplified for you so that you do not need to use the query language syntax see Figure 3 1 Using this method allows you to select the operators from a drop down list LION Bioscience Entry Creation Date between v 11
32. has been set up LION Bioscience The next sections describe these methods see sections 6 4 2 Interactive Tools p 141 and 6 4 3 Batch Tools p 142 6 4 2 Interactive Tools Tools that do not take long to run are usually run interactively This means they will be started immediately and run while you wait The Tool Invocation page Figure 6 2 will be displayed while the analysis is running e LION Help Center 7 Quick Select Query Custom i EE Databanks Form Tools Results Projects Views Information SRS Tool is currently running Please don t go back Whenever the execution finishes the results will be presented here Tool command was srsuser rice linux 7 bin blastall p blastx d srsdata flatfiles blast swissn v lt gt ir ir e Welcome to SRS 7 1 BLASTX JobName temp jobi SYAHI1KonQp RUNNING BLASTX JobName temp jobi SYAHIiKonOp RUNNING INDEXJOB Figure 6 2 Tool Invocation page The Query Result page Figure 6 3 will appear automatically on completion unless the show results automatically check box has been unticked 141 142 Analysis Tools Help Center O OT Results Projects 1 Information SRS Query BLASTX JobName temp job1 found 50 entries next CE rcu S ad Database selected results only BLASTX temp jobi swissnew 1 HMX STRPU EMBL MMNKX swissnew sp Q26656 HMX STRPU 9 unselected results only Result Options BLASTX temp jobi swissnew
33. he Use wildcards lv Get results of type Entry v Result Display Options 9 View results using SegSimpleView v or O Create a view Show 30 he results per page Ta da mara advuancad In a single field you can separate multiple values by amp Altext v Altext Alex v AlTex v Create a view Select the fields you want displayed in your view and choose the format Choose 1 or more fields ID Accession Number Primary Accession Number Description Gene Name Keywords Entry Creation Date s Sequence Format swiss Display As 9 Table O Wm _ Search List Imp Search j Figure 1 5 Standard Query Form for a query on the SWISS PROT databank 4 n the first field box select the Description field using the drop down list 5 Type kinase in the text box beside it Fields you can search You search terms In a single field you can separate multiple values by amp Descipion hres jara O d Olatet O O s jata O sx Figure 1 6 Search the Description field for kinase m Search 10 SRS Quick Tour 1 4 Sorting Results See section Sorting Results p 82 for more information Note If you want to know more about the chosen field click on the 6 icon beside it This will display the Field Informa tion page see also section Information Pages Field Infor mation in the Online Help Use the Back b
34. is regarded as comprising a sin gle element An asterisk indicates that the preceding group may be repeated zero or more times LION Bioscience Table 8 1 Regular expression operators Continued Operator Meaning A plus sign indicates that the preceding group may be repeated one or more times A question mark indicates that the preceding character or group of characters occurs one or zero times Table 8 2 Examples of regular expressions Expression Meaning j 8 This expression finds all three char acter strings that start with j 5 10 9 0 9 0 91 This expression finds all four digit numbers that start with 5 nif a el This expression finds the gene names nifa nifb nifc nifd nife mue ller This expression finds both muller and mueller Note Searches with regular expressions are sometimes slow since all the words in the index have to be searched 8 2 4 Searching Using Numerical Ranges In a numerical index whether it contains integers or reals it is possible to search numerical ranges A numerical index is only possible where there is a one to one relationship 161 162 SRS Query Language between entry and value e g sequence length creation date resolution A range can be specified using a single value or by two values separated by a colon The value on the left must be smaller than the value on the right To exclude a value from the range
35. of the gt lt Link Link keeping items in the set to the left of the gt a Link Get subtree defined by left operand hierarchical links gt Link Get leaf entries of the subtree defined by left operand hierarchical links LION Bioscience Logical Operators The logical operators OR AND amp and BUTNOT can be used to combine search words in an index search or to combine sets in a query The following figure illustrates the effects of the three operators in an expression of the form A operator B OR AND BUT NOT GD 4 A B A amp B AIB Figure 8 2 Logical operators in SRS Logical operations can only be performed between sets of the same type It is not possible for instance to combine a set of entries and a set of subentries see section 8 4 Entries and Subentries p 173 using logical operators In such cases an additional link operation must be specified see section 8 4 1 Links with Sets Containing Subentries p 174 Link Operators Link operators are unique to the SRS query language The two link operators lt and gt allow sets of data from different databanks to be combined Figure 8 3 shows two databanks A and B in which some entries in A have links to entries in B These links are processed to build link indices that provide the basis for the 169 170 SRS Query Language link operation The figure shows the results of two searches for links between set
36. only Complete entries oroteinChart Swissprot View Ls Swissprot List View Figure 5 2 Choosing a predefined view for results from the Standard Query Form 4 Click on the Search button Complete any further information e g if a separate win dow pops up lolx Smoothing steps 2 Red marker value jea76 af gt Warning Applet Window Figure 5 3 Chart controller window for proteinChart view 5 This will display the Query Result page with the results of your query displayed using the selected view see Figure 5 4 113 114 Views 9 LION Quick Searches Sele Databanks Help Center ct Custom Results Projects Views Information Apply Options to C selected results only unselected results only Result Options Launch analysis tool Bas Launch Show tools relevant to these Tools _ Link to related information Link Save Display Options View results using proteinChart Sort results by unsorted ascending C descending Show 30 results per page results Save results Printer friendly view Apply Display Options Query swissprot AllText oxidase found 1728 entries next SWISSPROT Description SWISSPROT 2NPD NEUCR 2 nitropropane dioxygenase ProtSequence 100 0 precursor EC 30 0 1 13 11 32 Nitroalkane oxidase I 2 NPD 70 0 60 0 ssas cocco
37. option is to use the Query Expression text box at the top of the Manage your Query Results page This option is discussed later see section 4 5 Expression Linking p 104 LION Bioscience 101 4 4 2 Finding Links from the Query Result Page This method is useful for searching for links from individual entries or groups of entries It is assumed that you have made your query as normal From the Query Result page choose those entries which are of interest and click the tisk button to display the Link page see section 4 3 Index Links p 95 Note You can choose whether to search for links to your results based only on the selected entries results selected only or based only on the entries results that are not selected unselected only items by setting the Apply Options To options This is particularly useful if you wish to find links for a large proportion of your results The Apply Options To options are usually set to unselected results only Example 4 2 Initiating a link from the Query Result page 1 Query EMBL for entries whose description field contains the word kinase EMBL entries will be displayed on the Query Result page 102 Links to Additional Data Quick Help Center 2 Searches Results Projects Information SRS Reset Query embl ALLTEXT kinase found 586050 entries next EMBL 4490
38. page 99 from query result page 101 link page finding 99 operators 105 query language 169 parent 175 procedure 95 list view 124 125 128 logical operators query language 169 manage manage your query results page 31 managing project manager page 47 projects permanent 46 temporary 42 multiple databanks searching 164 N non secure permanent projects 43 starting 44 numbers in indices search for 57 numerical ranges combining 163 searching query language 161 O open 52 operands 167 operators linking 105 169 logical 169 query language 168 regular expressions 160 using 171 order sorting results 82 overview 10 P page application invocation 25 29 30 application select 21 download options 32 entry 103 extended query form 65 field information 88 job status 145 link 11 manage your query results 31 query manager 17 20 99 query result 10 101 standard query form 62 start 2 view manager 1 14 view manager 2 15 pages query result 5 LION Bioscience parameters applications 23 parent links 175 passwords spaces 44 special characters 44 permanent projects 38 managing 46 non secure 43 secure 43 starting 44 project starting 2 projects administration 47 permanent 38 managing 46 non secure 43 secure 43 starting 44 project manager page 47 starting 39 switching 48 temporary 38 41 managing 42 starting 41 Q query 55 expression query 79 manage your query results page 31 sorting results 82 ov
39. property are retrieved because the annotation is often incomplete 8 5 Storing Intermediate Results in Sets If a query becomes very complicated it may be convenient to store an intermediate result into a set with a name which can be used later in the query This is particularly useful to save typing out the query several times but does not actually save a file This example is an index query in EMBL that is then linked to both SWISS PROT and SWISSNEW embl org escherichia coli gt SWISSPROT embl org escherichia coli gt SWISSNEW The EMBL index query is specified twice however it is possible to store the result of the index query in a set e g temp which saves duplicate typing of the index query The assignment operation must be within parentheses as shown temp embl org escherichia coli gt prosite temp gt SWISSNEW index search 157 Symbols range search 157 wildcard 59 string search 157 wildcard 59 A accessing analysis tools 138 administration projects 47 analysis tools 137 using 138 what are they 138 application invocation page 25 29 30 application select page 21 applications batch 142 invocation page 25 29 30 parameters 23 select page 21 applications See analysis tools apply views 111 B batch applications 142 applications batch queued 24 not batch queued 27 browse index 86 C characters special databank group names 164 LION Bioscience INDEX f
40. query sequence to use Both b as Output Options Search Parameters Number of hits and alignments to show 50 Filter query sequence C Number of best hits from a region to keep Penalty for a nucleotide mismatch 3 100 Reward for a nucleotide match 1 The E value 10 000000 word size Default Perform gapped alignment lv Cost to open a gap Default Cost to extend a gap Default v Use lowercase filtering of query sequence Figure 1 18 Default settings for the Launch page Note If you want to know more about any of the tools click on the More Info link beside any of the tools listed on the Tool Select page 6 When you run a tool you can set values for the run time options on the Launch page For this example use the Default parameters More information about tool options is available in chapter 6 Analysis Tools p 137 23 24 SRS Quick Tour In addition for tools that will be sent to a batch queue there is a drop down list that allows you to choose which batch queue where there is more than one batch queue available to you This is not shown in Figure 1 18 because there is only one batch queue available on the installation used Note Depending on how your installation is set up the tool may be run as a batch job using a batch queueing system or it may be run interactively Figure 1 18 shows that BLASTN will be run as a batch job for
41. results from an analysis can be reached from the Job Status page see Figure 6 6 This page is reached by clicking on the results hyperlink or on the H icon on the Tool Invocation page Help Center O LION Z AEE aech Results Projects Information SRS Job Options List of Batch Jobs Job Name Status Start Date Results from Result Set Queue Name Options are applied to selected jobs only temp blastn 1 IM ee BLASTN Q2 50 priority m klee batch Delete jobs Delete View job results using Complete entries v View Run job again with different options Edit Options SRS Release 7 1 Copyright amp 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 6 6 Job Status page When a job has completed the job name becomes a link to the results of your analysis and the hourglass fd becomes an hourglass with a green tick B4 Clicking on the hyperlink for the job that has just run e g temp blastn Will display the Entry page containing the results LION Z Quick Searches SRS selected results only 9 unselected results only Result Options Launch analysis tool HmmBuild Launch Show tools relevant to these results Tools Link to related information Link Save results Save Display Options View results using Blast View vi Show 30 results per page Printer friendly view C Apply Display Options Select Databanks
42. the Link page in the Link Options box Link Options Select the databanks you want to search for related information s Find related entries Refine Query show only results with related entries Cy Show only results without related entries m _ Search Figure 4 7 Link Options The meanings for these options are as follows Find related entries This returns entries from other databanks which have links with entries in the current query Refine Query show only results with related entries This limits the query so that it includes only the entries from the original query which are linked to all of the selected databanks Show only results without related entries This limits the query so that it includes only the entries from the original query which do not have links to the specified databanks LION Bioscience 4 4 Getting to the Link Page It is possible to initiate a linking operation from many pages These include the Manage your Query Results page see section 4 4 1 Finding Links from the Manage your Query Results Page p 99 the Query Result page see section 4 4 2 Finding Links from the Query Result Page p 101 and the Entry page see section 4 4 3 Finding Links from the Entry Page p 103 4 4 1 Finding Links from the Manage your Query Results Page This method is useful for finding links for complete queries You can search for links from a single query or from multiple
43. the applications that are available on your SRS installation However you will have to enter your own sequence data on the Launch page Section 1 7 Using Analysis Tools p 20 explains how to start a tool The remainder of this chapter gives further LION Bioscience information on the use of tools and further details of the differing behavior of interactive and batch tools 6 3 Launch Page 6 3 1 Tool Parameters amp LION Quick Searches Select Databanks Help Center O Results Projects Information Result Display Options View results using Blast View v Show 30 M results per page Show results automatically v Parameter set options Save current parameter set as BlastX More Info Job name Database to search i Launch temp SWISSPROT Updates v Wb Launch EMBL MMNKX begin 4 1 11 21 31 41 51 6i 71 81 91 101 111 d gtgtcagagcagcacaggtcaccagagcttctgagcaaaaagaggagacctcaagactat enc 1972 121 131 141 151 161 171 cttcccattggccaagagagaaagctttcagggcacaggcaagaggaggagggcaccgag v lt gt Strand of query sequence to use Both Y Codon Translation table Standard Genetic Code Y Output Options Search Parameters Filter query sequence Number of hits and alignments to show 50 Number of best hits from a region to keep 100 Scoring matrix BLOSUM62 v The E value 10 000000 word size Default v Perform gapped
44. the des description field of the protein databank PIR A search string may be a single search word or several words separated by logical operator s see section 8 3 4 Operators p 168 Parentheses may be used to create a group which will be treated as a single operand see Example 8 1 Search strings Wildcards and regular expressions may also be used see section Wildcards p 159 and section Regular Expressions p 159 Example 8 1 Search strings To search the keywords field of the EMBL databank for insulin you might enter emb1 key insulin To search the description field of the EMBL databank for entries which include acetylchol and receptor but remove any entries that contain muscarinic you might enter embl des acetylchol amp receptor muscarinic To search the authors index field of the SWISS PROT databank to look for entries containing sanger f but not coulson a you might use a query like swissprot aut sanger f coulson a LION Bioscience Wildcards Wildcards are useful if for example you wish to search for a group of words e g all words starting with cell and ending with ase or if it is unclear how a word is spelt in a databank SRS uses two types of wildcard Matches zero or more characters of any value Matches one character of any value Any number of wildcards can be placed anywhere in a search word Note Pl
45. the root databanks and the linked databanks that should be displayed View Manager page 2 The format of some fields such as Sequences View Man ager page 2 In selecting the root databanks for a view you specify two important things Firstly the view will only be available for queries and result sets based on these databanks Secondly the available fields from the root databanks will be those that are common across all of the root databank selections Therefore it is sensible to select databanks that have similar fields when you are creating a new view To Create a View 1 Click on the Custom Views tab This will take you to the View Manager page 1 2 Name the view by entering a suitable name in the View name text box LION Bioscience Create View Options View name myTestView Display results as C table list Figure 5 18 Create View Options box showing naming of a view and the table and list view options Note lt is better not to include spaces and other special char acters in names as some systems do not handle them prop erly Use an underscore or start new words with a capital letter instead 3 Choose whether the new view will be displayed using a table or list format 4 Choose whether you wish to choose from all available fields in the selected databanks or just the common ones Show fields from All fields in databanks Common fields only Figure 5 19 Selecting fields 5 Select the da
46. this SRS installation but this may not be the case on your installation Section Running a Batch Queued Tool p 24 demonstrates how to run a batch appli cation while section Running an Interactive Tool p 27 describes how to run an interactive application 1 7 1 Running a Batch Queued Tool 1 Click the taunch_ button to start the tool running see Figure 1 19 LION Bioscience Ud LION z Help Center Select Query Quick Custom Searches Databanks Form Views Information Tools Results Projects Tool was submitted to Queue blast m sisley batch Tool command blastall p blastn d srsdata flatfiles blast emblnew i temp blastn 1 in lt gt Use Batch job status page to view the results Figure 1 19 Tool Invocation page Note The kd icon that appears at the top left of your SRS window indicates that you have a batch job running See section 6 4 3 Batch Tools p 142 for more information on this icon and others used when running batch applications 2 Click on the kh at the top left corner to see the Job Sta tus page which will show the status of any batch queue jobs you have run v LION 9 4 Help Center 7 Select Query Quick Custom Searches Databanks Form Views Information Tools Results Projects SRS Job Options List of Batch Jobs Job Name Status Start Date Results from Result Set Queue Name Options are applied to 18 Mar 2003 12 40 selected jobs only temp blastn 1
47. use them later Projects p 41 for more Click the Results tab to take you to the Manage your NICE MENON Query Results page Here you can choose which queries you want to save 32 SRS Quick Tour 2 Select a query that you want to save by ticking the check box beside it D Help Center LION pacea ANT ay Tools f Results Projects TE Information SRS Reset Search using a query expression Results Options Options are applied to selected queries only x Result History m _Search Save results 2 Name Type Total No From No Query Expression Comment Delete results Delete Select options to save data 39 BLAST a 30 BLASTX JobName temp lt gt Combine queries Q2 workflow 3 EMBL 3 EMBL alltext mmnkx with amp AND v lt gt Combine Zoi workflow 586050 EMBL 586050 rwmL allcexc kinase lt gt Find related info Link i Results Display Options View results using Complete entries v Show 30 v results per page Rerun Query Figure 1 27 Select a query to save 3 Click the Save button to display the Save Options page 4 Use the Save Options page to specify what is saved the way the output is saved and where it goes to a text file or to the screen LION Bioscience P LION Help Center 2 Quick Select Query Custom Searches Databanks Form Tools Results Projects Views Information SRS Reset Saving Query EMBL alltext kinase 586050
48. 1 getz Usage p 151 and chapter 8 SRS Query Language p 155 Here are a few examples To retrieve a list of entries from the SWISS PROT databank that have azurin mentioned in the description you might enter getz swissprot des azurin If you want to perform the same search as above but retrieve the complete entries use the e argument getz e swissprot des azurin To retrieve the sequence for the entries using the FASTA format type getz f seq sf fasta swissprot des azurin To specify that the results should be sorted and the sort direction include sort and sortDir arguments in your command getz swissprot id p sort sl acc sortDir 01 7 1 1 getz Usage LION Bioscience Section 7 1 1 getz Usage p 151 explains more about the arguments The following table lists the options available for command line SRS These options can be used to refine your getz queries Alternatively to find out more about getz use the command getz help Table 7 1 Common getz options Option Default Function help Help with getz e FALSE Prints the entire entry t FALSE Copy the complete text annotation part of the entry d FALSE Copy the data e g sequence part of the entry zi FALSE Print the tokens that would be generated for indexing f string TE Include fields in entry list vf string Mt List of fields that will be placed into a table view w FALSE
49. 1535 44901535 NCMSB1T3 Mycelial Neurospora crassa cDNA clone NMSB1 5 347 os ae end mRNA sequence selected results only zm at EMBL 44901632 NCM4G1T3 Mycelial Neurospora crassa cDNA clone NM4G1 5 9 unselected results only 44901632 end mRNA sequence 536 EMBL 44901739 44901739 NCPSC11T7 Perithecial Neurospora crassa cDNA clone 473 Result Options NPSC113 end EMBL 44901740 44901740 NCM6F2T3 Mycelial Neurospora crassa cDNA clone NM6F2 5 442 Launch analysis tool end mRNA sequence f EMBL 44901762 NCM1C7T7 Mycelial Neurospora crassa cDNA clone NM1C7 3 BlastN v taunch AA901762 ond mRNA sequence 2H Show tools relevant to these EMBL 44901817 NCC1G8T Conidial Neurospora crassa cDNA clone NC1G8 3 4 901817 end mRNA sequence qun results Tools Em EMBL 44901858 AA901858 NCC1E9T 7 Conidial Neurospora crassa cDNA clone NC1E9 3 486 Link to related information end MRNA sequence EMBL 44901859 NCC2D1T7 Conidial Neurospora crassa cDNA clone NC2D1 3 Link AA901859 end MRNA sequence 608 Save results Save EMBL 44901875 A 901875 Li dd Perithecial Neurospora crassa cDNA clone NP4B7 3 555 EMBL 44901876 NCC4C8T Conidial Neurospora crassa cDNA clone NC4C8 3 Display Options pASU1B78 end mRNA sequence in EMBL 44901892 NCC1A1T7 Conidial Neurospora crassa cDNA clone NC1A1 3 View results using aia end mRNA sequence Ls 5 EMBL 44901893 NCC1D8T Conidial Neurospora crassa cDNA clone NC1D8 3 SeqSimpleView Ni 54901893 ond m
50. 1x qe Please type your user name and password Site mallard lionbio co uk Realm session UserName user Password Save this password in your password list Cancel Figure 2 4 SRS secure password protected account Log in dialog box Explorer User Prompt x Script Prompt Enter your SRS user name Cancel Figure 2 5 SRS non secure account Log in dialog box 2 For secure account access complete the login information The web browser will prompt you to give a User Name and Password You may need to ask your SRS Adminis trator for these because they may not be the same as your system account ID and password For non secure account access enter your user name at the prompt 3 Click ma In either case the Project Manager page is displayed From here you can continue working with the most recently used project switch to another project or create a new project This is described in section 2 3 2 Managing Permanent Projects p 46 and section 2 4 Using the Project Manager p 47 45 46 SRS Projects 2 3 2 Managing Permanent Projects If you followed the steps outlined in section 2 3 1 Starting a Permanent Project p 44 the Project Manager page will be displayed see Figure 2 6 The Project Manager page provides you with the necessary tools to manage your SRS projects It allows you to move queries or views between projects save and open projects delete unwanted projects
51. 3E ORYSA 3D precursor EC 3 2 1 1 1 4 alpha D glucan Created Last sequence update Last annotation update P27934 A lpha amylase isozyme glucanohydrolase AMY1 4 OR AMY3E 01 AUG 1992 Rel 01 AUG 1992 Rel 23 15 DEC 1998 Rel 37 SWISSPROT AMC1 ORYSA 3E precursor EC 3 2 1 1 1 4 alpha D glucan 23 Created Last sequence update Last annotation update P27940 Alpha amylase isozyme C precursor EC 3 2 1 1 1 4 alpha D glucan glucanohydrolase Isozyme 1B AMYC OR AMY1B 01 AUG 1992 Rel 23 01 AUG 1992 Rel 23 15 DEC 1998 Rel 37 SWISSPROT AMY1 AEDAE Created Last sequence update Last annotation update P53354 Alpha amylase I precursor EC 3 2 1 1 1 4 alpha D glucan glucanohydrolase AMY1 OR AMY I 01 OCT 1996 Rel 34 01 OCT 1996 Rel 34 01 OCT 1996 Rel 34 SWISSPROT AMY1_ AERHY Created Last sequence update Last annotation update P22630 lpha amylase precursor EC 3 2 1 1 1 4 alpha D glucan glucanohydrolase 01 AUG 1991 Rel 19 01 AUG 1991 Rel 19 01 FEB 1995 Rel 31 Created Last sequence update Last annotation update SWISSPROT AMY1 DICTH P09961 33503 1 4 Figure 5 16 Query Result page showing a list view Creating Views from the Extended Query Form On the right of the Data Area is a column entitled Create a view see Figure 5 17 This contains check boxes one for each datafield which
52. 5 AMP activated protein kinase beta 1 subunit P80387 AMPK beta 1 chain AMPKb 40 kDa subunit 122 Fragment SWISSPROT AAKC RAT 5 AMP activated protein kinase beta 2 subunit Q9QZH4 amPK beta 2 chain Zu I SWISSPROT AAKG BOVIN 5 AMP activated protein kinase gamma 1 subunit Fs81ug AMPK gamma 1 chain AMPKg 330 IO SWISSPROT AAKG PIG 5 AMP activated protein kinase gamma 1 subunit Q09138 AMPK gamma 1 chain AMPKg 38 kDa subunit 133 Fragments fe n n A A SWISSPROT AAKG RAT S AMP activated protein kinase gamma 1 subunit Penaga AMPK gamma 1 chain AMPKg 330 I SWISSPROT AAKI HUMAN 5 AMP activated protein kinase gamma 3 subunit Qouorm I amp MPK gamma 3 chain AMPK gamma3 464 f Fi 5 A 3 O SwISSPROT AAKI PIG S AMP activated protein kinase gamma 3 subunit Q9MYP4 AMPK gamma 3 chain AMPK gamma3 464 SWISSPROT ACEK ECOLI Isocitrate dehydrogenase kinase phosphatase IDH P11071kinase phosphatase EC 2 7 1 116 EC 3 1 3 Bzg SWISSPROT AFC2 ARATH P51567 Protein kinase AFC2 EC 2 7 1 427 SWISSPROT AFC3 ARATH P51568 Protein kinase AFC3 EC 2 7 1 400 I SWISSPROT AFSK STRGR P54742 Serine threonine protein kinase afsK EC 2 7 1 807 Select Databanks Query swissprot Description kinase found 3741 entries LION Bioscience Help Center Projects Information
53. Appends a wildcard to each search word lb lt n gt 0 Number of first entry in set to be viewed 151 152 Command Line SRS Table 7 1 Common getz options Continued Option Default Function 11 lt n gt 0 Number of entries to be viewed in one go 1v FALSE List all values that match the query lv FALSE List all values that match the query plus the number of entries for each match lmin n 0 List only values that occur at least the specified number of times Use together with 1v c FALSE Report the number of entries that were found but not the entries themselves info FALSE Prints info about the specified databank libs FALSE Prints a list of all active databanks view lt string gt rs string cs string sf string af string Name of view to be used when displaying entries String of one or more characters to separate records in view String of one or more characters to separate columns in view Format of sequence output file Format of sequence alignment output file LION Bioscience Table 7 1 Common getz options Continued Option Default Function html FALSE Select HTML format for output ascii TRUE Select ASCII format for output off FALSE Accesses the off line version id string sort lt string gt sortDir lt string gt of a databank The user ID or filename associated with a WWW ses sion The name of the field on wh
54. BL A21640 in other databanks Databanks Available to Link to Link Options Expand all Collapse all Select the databanks you want to search for related information To Parent Entry m Search EMBOSS Results Sequence databanks complete n all Displey Gotlon EMBL SWISSPROT Sequence databanks subsections SeqRelated Tool Results View results using default view M Show 30 results per page Figure 4 5 The Link page for linking initiated from the Entry page 1 Choose the databank in which you wish to search for links by ticking the check box to the left of it 2 Choose the appropriate Link Option see section 4 3 2 Link Options p 98 3 Click the Search button to display the results P LION Help Center Quick Select Query Custom Searches Databanks Form Tools Results Projects Views Information SRS Reset Query embl ALLTEXT a21640 found 1 entries Apply Options to EMBL Accession Description SegLength v EMBL 421640 421640 protein kinase gene 1403 selected results only unselected results only Figure 4 6 Typical Query Result page for a linking request 97 98 Links to Additional Data 4 3 2 Link Options Unless you have initiated your search for links from the Entry page there are several options for choosing the set of entries for which you wish to search These are listed on
55. Complete entries SeqSimpleView Swissprot View Swissprot List View per page Printer friendly view T Apply Display Options Query swissprot AllText oxidase found 1728 entries Apply Options to SWISSPROT next Description ProtSequence SWISSPROT 2NPD NEUCR 2 nitropropane 14 dioxygenase precursor EC 1 13 11 32 1 20 Nitroalkane oxidase 2 NPD 1 0 og 0 60 0 4 0 0 100 0 200 0 300 0 400 0 SWISSPROT 2NPD WILMR 2 nitropropane 44 dioxygenase EC 13 1 13 11 32 Nitroalkane oxidase 1 20 2 NPD 14 ooooonoc mutuo 0 0 100 0 200 0 300 0 400 0 swissprot acc3 LYCES 1 14 aminocyclopropane 1 carboxylate oxidase homolog 1 20 Protein E8 1 0 08 0 60 ee 0 0 100 0 200 0 300 0 400 0 Figure 5 5 Selecting the view on the Query Result page 1 Select the view you want to use from the drop down list 2 Click the Apply Display Options button The Query Result page will be refreshed so that it dis plays the results using the selected view LION Bioscience Note lf you select a number of entries prior to clicking the Apply Display Options button then only those entries will be shown when you click feply Display Options J Applying a View From the Entry Page For most of the Entry pages you will come across you will have a simple choice of viewing the entry in a text format ora databank spec
56. EMBL A21640 Entry Options Molecule Type DNA Sequence Length 1403 Launch analysis tool r Entry Division VRL BlastN v Launch VERONA 421640 Link to related information Sequence Version A21640 1 Link Creation Date 22 JUL 1994 Modification Date 22 JUL 1994 Save entry TER View Printer Friendl Description protein kinase gene Keywords Organism Pseudorabies virus Organism Viruses dsDNA viruses no RNA stage Herpesviridae Alphaherpesvirinae Varicellovirus Classification Organelle References 1 MUTANT PSEUDORABIES VIRUS AND VACCINES CONTAINING THE SAMEPatent number WO9102795 A 3 07 MAR 19091 Position 1 1403 GOA P24381 P24381 SWISS PROT P24381 KR1 PRVN3 Figure 4 2 The Entry page for the EMBL entry with accession number A21640 3 Scroll through the entry until you find a hyperlink e g in the entry shown in Figure 4 2 there is a hypertext link to SWISS PROT This will have a unique identifier acces sion number P24381 in figures 4 2 and 4 3 LION Bioscience Database Cross references GOA P24381 P24381 SWISS PROT P24381 KR1 PRVN3 Figure 4 3 Database Cross references entry showing a hypertext link to SWISS PROT If you do not find a link in your chosen entry try choosing a different entry from the Query Result page 4 Click the hypertext link to view the Entry page for the SWISS PROT entry 4 3 Index Links 4 3 1 Searching for Data using Index Links It is assu
57. E_features EMBLRELEASE_reference EMBLRELEASE_counter EMBL Updates zl Delete View B Names only gt Figure 5 21 View Manager page 1 EMBL_reference EMBL_features EMBL_counter SWISSPROT SWISSPROT reference SWISSPROT comment SWISSPROT feature SWISSPROT counter EMBL Release EMBLRELEASE features EMBLRELEASE reference EMBLRELEASE counter EMBL Updates xl IN Create New View Delete View LION Bioscience SRS will display the View Manager page 2 on which you can select the specific fields for your view By default it can be changed on View Manager page 1 the top box contains the fields which are common to all of the root databanks selected on the previous page There are additional boxes below this for each linked databank you chose Using these check boxes select the fields that you would like to see in your view 8 Select the fields you would like to display in your view by ticking the check boxes beside the relevant fields 133 134 Views SWISSPROT Select the datafields you want displayed in your F ID AccNumber Prim ccNumber M Description view using the checkboxes GeneName D Keywords DateCreated M LastSequenceUpdate Wiki md myileeiemc LastAnnotationUpdate Organism D Taxon NCBI TaxId maite save Organelle ProteinID checksum DbName DBxref SegLength Sequence fasta E Fields of subentry Reference Authors Title
58. IiKonQp RUNNING INDEXJOB Figure 1 24 Tool Invocation page for an interactive tool 5 When the tool finishes running the results will be dis played automatically See Figure 1 25 29 30 SRS Quick Tour Help Center O Me MV Results Projects Information SRS Query BLASTX JobName temp job1 found 50 entries next HERES PERSE Epl 751 ee Database selected results only BLASTX temp jobi swissnew 1 HMX STRPU EMBL MMNKX swissnew sp Q26656 HMX STRPU 9 unselected results only Result Options BLASTX temp jobi swissnew 2 HK32 MOUSE EMBL MMNKX swissnew sp P97503 HK32 MOUSE Launch analysis tool BlastP v Launch Show tools relevant to these BLASTX temp job1 swissnew 3 HK32 HUMAN EMBL MMNKX swissnew gt sp P78367 HK32 HUMAN results Tools Link to related information Link Save results SIVE BLASTX temp jobi swissnew 4 HM1D DROAN EMBL MMNKX swissnew gt sp P22544 HM1D DROAN 7 x BLASTX temp jobi swissnew 5 HMX2 COTJA EMBL MMNKX swissnew sp P23410 HMX2 COTJA Display Options View results using Blast View al BLASTX temp jobi swissnew 6 NK2E XENLA EMBL MMNKX swissnew sp P42583 NK2E XENLA BLASTX temp jobi swissnew 7 HMX2 CHICK EMBL MMNKX swissnew gt sp P28362 HMx2 CHICK Show 30 results per page BLASTX temp jobi swissnew 8 SAX1 MOUSE EMBL MMNKX swissnew sp P42580 SAX1 MOUSE Printer friendly view C
59. MBL 429801 429801 Pyruvate kinase gene altered 49 EMBL A32502 432502 Synthetic NDP kinase protein primer 17 Sort results by Accession Number m EMBL A32505 A32505 D discoideum NDP kinase gene 530 9 ascending EMBL 432507 32507 Synthetic N terminal fusion NDP kinase gene 184 O descending EMBL MMAD0144 mg31a09 r1 Soares mouse embryo NbME13 5 14 5 Mus AADOD144 musculus cDNA clone IMAGE 425368 5 similar to gb M74149 600 Sh 30 al It Mouse creatine kinase B gene complete cds MOUSE D SERE mRNA sequence El parere EMBL MMADD177 mg33h05 r1 Soares mouse embryo NbME13 5 14 5 Mus es S A000177 musculus cDNA clone IMAGE 425625 5 similar to gb 249877 474 Printer friendly view C M musculus syk mRNA for protein tyrosine kinase MOUSE mRNA sequence Apply Display Options EMBL MMADD178 mg33h08 r1 Soares mouse embryo NbME13 5 14 5 Mus musculus cDNA clone IMAGE 425631 5 similar to gb U07358 Figure 4 1 The Query Result page with results sorted by Accession Number see section 3 6 Sorting Results p 82 94 Links to Additional Data Linked data in the entry 2 Click on the hypertext link beside an entry to view the entire entry P LION Help Center 2 Custom Views Quick Select Query Searches Databanks Form Text Entry EmblEntry Tools Results Projects Information Reset Entry Information Goto General Description References Cross references Features Seguence Entry from EMBL General Information Entry Name
60. O Quick c r Custom Searches Databanks Tools Results Projects Views Information SRS Reset 7 Yalues in SWISSNEW Browse Options Value No of Entries More Values sercai 4 8 Make Query I serca2 serca3 3 Yalues in SWISSPROTRELEASE Value No of Entries sercai 6 serca2 8 T serca3 5 Figure 3 26 Browsing the Description field index on the Browse Index page 3 Tick the check boxes beside the resultant terms that best match your needs and click the Hake Query button This returns entries that match the selected terms 3 7 3 Getting to the Field Information Page There are a number of routes you can use to get to the Field Information page The common routes are detailed here From the Query Forms On the Standard Query Form there is an icon beside each field box Choose the field of interest from the drop down list and click on the icon LION Bioscience Fields you can search Your search terms In a single field you can separate multiple values by amp m Search Orqanism Name v GES S SSS Ama wl 0C elus O x ela z Figure 3 27 Standard Query Form showing use of the icon to access the Field Information page On the Extended Query Form each of the datafields is a hyperlink to the Field Information page Simply click on the hyperlink for the field of interest In a single field you can separate multiple values by amp m Search AllTex
61. Query swissprot Authors smith gt parent amp swissprot Authors jones gt next parent found 1336 entries SWISSPROT accession __Description _ SeqLength C SWISSPROT AATM LUPAN Aspartate aminotransferase P2 mitochondrial P26563 precursor EC 2 6 1 1 Transaminase A 454 Fragment SWISSPROT AMYG YEAST Glucoamylase intracellular sporulation specific P08019 EC 3 2 1 3 Glucan 1 4 alpha glucosidase 549 1 4 alpha D glucan glucohydrolase SWISSPROT AMYH YEAST Glucoamylase 1 S2 precursor EC 3 2 1 3 P08640 Glucan 1 4 alpha glucosidase 1 4 alpha D 1367 glucan glucohydrolase I SWISSPROT ARi16 YEAST P40518 ARP2 3 complex 16 kDa subunit P16 ARC 154 I SWISSPROT AXL2 YEAST P38928 AXL2 protein precursor SRO4 protein 823 M SWISSPROT BNR1 YEAST P40450 BNI1 related protein 1 1375 SWISSPROT COPE YEAST Coatomer epsilon subunit Epsilon coat mE EMBED P40509 protein Epsilon COP 296 SWISSPROT DA81 YEAST Transcriptional activator protein DALS1 ee ee ee EAE P21657 Regulatory protein UGA35 azo Figure 3 9 Query Result page showing the results of a query for entries using the References Authors subentry fields using two separate text boxes to search on the Standard Query Form Using two separate text boxes for the subentries search retrieves all entries containing references by Smith and by Jones including those where there are no papers which were co authored by
62. RNA sequence inl Sort results by C EMBL AA901894 NCC1F2T Conidial Neurospora crassa cDNA clone NC1F2 3 B A 901894 end mRNA sequence 528 unsorted v ER EMBL AA901895 paggigas NCC2H6T7 Conidial Neurospora crassa cDNA clone NC2H6 3 524 ascending pesca Dag pe end mRNA sequence descending EMBL A4901896 NCC3D6T7 Conidial Neurospora crassa cDNA clone NC3D6 3 mE oris end mRNA sequence 325 Show 30 results EMBL A4901987 NCC4E1T7 Conidial Neurospora crassa cDNA clone NC4E1 3 i0 Erw iced ARHUTSBZ end mRNA sequence 348 per page s EMBL AFOS6142 AF056142 rice blast fungus mRNA from nitrogen starved d T ndlvii o Zooo O AF056142 mycelial culture Pyricularia grisea cDNA clone PU40 similar to 647 Printer friendly view protein kinase C MRNA sequence Apply Display Options C EMBL AI391970 NCC1F3T3 Conidial Neurospora crassa cDNA clone NC1F3 5 APP Spray Options 41391970 similar to casein kinase II alpha catalytic subunit a 552 carinafrhrannina nrntain lin aca mPNA caniianca Figure 4 9 The Query Result page 2 Select the entries of interest by ticking the check boxes beside them 3 Click on the isk button This will display the Link page see section 4 3 Index Links p 95 LION Bioscience 4 4 3 Finding Links from the Entry Page This method is useful for linking from individual entries It is assumed that you have made your query as normal When the Query Result page appears choose one of the
63. RS Quick Search page displays the current project ID 2 Forthis tour a temporary project will be used Such a project will be started for you as soon as you start to make a query or select a databank you do not need to start a temporary project explicitly SRS Quick Tour 1 3 SRS Queries 1 3 1 Making a Query using SRS Quick Search Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms Quick Searches can be performed from either the Start page when you first open SRS or the SRS Quick Search page when you are already in a project Quick Text Search 1 You should already be on the Start page if you are not for any reason click on the Quick Searches tab This will take you to the SRS Quick Search page and you can per form the same queries from there 2 Select Protein Sequences from the Get drop down list This tells SRS to search the SWISS PROT databank and this is indicated below the drop down list 3 Type dehydrogenase in the matching text box to tell SRS what you want to find LION Bioscience Quick Text Search Search Tips Get Protein Sequences matching dehydrogenase Searches Databanks SWISSPROT mb Search Figure 1 2 Quick Text Search box showing a search for Protein Sequences SWISS PROT entrie
64. SRS USER GUIDE Copyright c 2003 LION bioscience AG LION All rights reserved LION Bioscience SRS 7 1 Documentation This manual as well as the software described in it is furnished under license and may only be used or copied in accordance with the terms of such license The information in this manual is furnished for information only is subject to change without notice and should not be construed as a commitment by LION bioscience AG LION bioscience AG assumes no responsibility or liability for any errors or inaccuracies that may appear in this book Except as permitted by such license no part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical recording or otherwise without the prior permission of LION bioscience AG Comments about the documentation are welcome at documentation uk lionbioscience com For customer support issues please e mail support uk lionbioscience com TABLE OF CONTENTS CHAPTER 1 SRS Quick TOUR 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 CHAPTER 2 SRS PROJECTS 2 1 LION Bioscience E E EA EEE E E Ea 1 Introduction iuo ikeeR E one RAS SERERE ona RAD 2 Starting an SRS Project 22 2 2 2 00 e eee eee eee eee 2 SRS Queries 5 25220 SUAE a e SR CRI et AS 4 Making a Query using SRS Quick Search 4 Making a Query Using the Standard Query Form 7
65. Select Query j Custom i Searches Databanks Form Tools Results Projects Views Information SRS Reset search SWISSPROT Search Options Fields you can search Your search terms In a single field you can separate multiple values by amp m Search Combine search terms with amp AND v AllText v AllText v Use wildcards lv e AlTex v Get results of type AllText v Entry v Result Display Options Create a view Select the fields you want displayed in your view and choose the format 9 View results using SeqSimpleview Choose 1 or more fields Display As Table List or ID Accession Number Se 7 k quence Format O Create a view Primary Accession Number swiss M Description Show 30 v at Moma eywords VREEIMIESISISY eS Entry Creation Date v TETY To do more advanced queries use the Extended Query Form Figure 3 4 Standard Query Form 1 From the Select Databanks To Search page select the databank you want to search by ticking the check box to the left of a databank name 2 Click the Standard Query Forn button from the Query forms box This will display the Standard Query Form Figure 3 4 3 Enter the search phrase s See section 3 1 Search Terms p 56 In each of the four search rows specify the field to be searched using the left hand drop down list and enter the 63 Querying with SRS search word or phrase in the corresponding righ
66. Smith and Jones Figure 3 10 shows an entry from the above search 72 Querying with SRS References 1 Tarver A P Clark D P Diamond G Russell J P Erdjument Bromage H Tempst P Cohen K S Jones D E Sweeney R W Wines M Hwang S Bevins C L Enteric beta defensin molecular cloning and characterization of a gene with inducible intestinal epithelial cell expression associated with Cryptosporidium parvum infection Infect Immun 66 1045 1998 Medline 98147718 PubMed 9488394 Position sequence from n a Comment tissue small intestine 2 Selsted M E Tang Y Q Morris W L McGuire P A Novotny M J Smith W Henschen A H Cullor J S Purification primary structures and antibacterial activities of beta defensins a new family of antimicrobial peptides from bovine neutrophils J Biol Chem 268 6641 1993 Medline 93203264 PubMed 8454635 Position sequence of 15 67 Comment strain hereford tissue neutrophils Figure 3 10 Entry page showing that some entries reference only papers that are not co authored by Smith amp Jones SWISS PROT accession number P46161 In effect this search looks for reference subentries that contain smith or jones It then takes the entries for each of the references matching the criteria to create two lists of entries one for smith and one for jones It then combines those seeking only those which are in both lists Searching for Entries which Reference Papers tha
67. The Save As dialog box 1 9 Review LION Bioscience 7 Select a location for the file and type a suitable name Note You should not use filenames which contain spaces or other special characters because these can cause problems on some systems Use an underscore or start new words with capital letters instead 8 Click 5 to save the file 9 Click the _ Ses button on the Download Complete dia log if necessary You have now completed a brief overview of the key features of SRS and should be ready to start using it on your own You should now know how to start an SRS project be able to perform a query using SRS link your query results to other databanks change the way in which your results are displayed by creating your own view run an application and save your working project If you want more information on any particular subject refer to the relevant chapter 35 36 SRS Quick Tour CHAPTER SRS PROJECTS All the work you do using SRS will be within projects These are simply a way of keeping related work together and any queries views etc that are created in a project will be stored in the project history This chapter introduces SRS projects By the end of this chapter you will have learned more about The benefits of using temporary and permanent projects How to start or return to a project Features that are available in permanent projects How to make temporary project data available
68. They may need to create an account for you 43 44 SRS Projects Note It is important that spaces and other special characters are not used in usernames or passwords because some systems do not handle them properly Use an underscore or start new words with a capital letter instead 2 3 1 Starting a Permanent Project Secure or Non Secure When you start a permanent project your system will determine whether it is set up for secure or non secure accounts This was determined when SRS was installed and you cannot choose at this point whether to use a secure or a non secure account This section describes how to open a permanent project by entering your user account SRS will automatically create a new permanent project within your account if you are entering it for the first time If you are re entering an existing account then the projects within that account will be available to you To start or return to a permanent project 1 Click the Start a Permanent Project link on the Start page The system will display a Log in dialog allowing you to log in to your account Typical dialogs for secure and non secure accounts are given in Figure 2 4 and Figure 2 5 respectively Note The dialog boxes shown throughout this manual were generated in the Windows32 version of Internet Explorer 5 The dialog boxes you see may look different depending on your system and web browser LION Bioscience Enter Network Password 2
69. a swissprot AllText alcohol amp swissprot AllText dehydrogenase Q2 swissprot AllText dehydrogenase v Embl_View FT Q1 swissprot AllText alcohol Figure 2 7 Choosing items to be copied 49 50 SRS Projects 2 Choose the project to which you want the items to be cop ied using the drop down list in the Project Options box projecti Options Save to desktop Save Rename project project Rename Delete project Delete Copy selected items to project v Copy roject2 ierra Figure 2 8 Choosing a project to which to copy items 3 Click on the ep button to copy the items This will copy the selected queries and views to the chosen project and switch to using that project 2 4 4 Saving a Project If you want to share a project with other users or if you want to move a temporary project to a permanent project list you first need to save a file containing the project work to your local disk To save a project 1 Make it the current project See section 2 4 2 Switching to Another Project p 48 2 Click the Save button in the Project Options box LION Bioscience 3 Select Save this file to disk when prompted xl p Some files can harm your computer If the file information below LY looks suspicious or you do not fully trust the source do not open or save this file File name wgetzca635071 File type From mallard Would you like to open the file or s
70. acing a wildcard at the start of a word or string may increase the response time because all words in the index have to be checked against your string Regular Expressions In addition to the use of wildcards it is also possible to enter regular expressions directly Regular expressions must appear within forward slashes Some characters have a special meaning these must be prefixed with a backslash Y to indicate that the specified character is to be matched literally 159 160 SRS Query Language Tables 8 1 and 8 2 respectively list typical regular operands and examples of their use Table 8 1 Regular expression operators Operator Meaning A A caret is used to mark the start of a string For example phos will find all words begin ning with phos e g phosphate A dollar sign s is used to mark the end of a string For example ases will find all words ending with ase e g kinase A dot indicates any single character Characters enclosed in square brackets are regarded as a set any of which can be matched For instance matches an open ing or closing parenthesis Character ranges can be specified using a hyphen e g o 9 matches any single digit A caret in front of the character set after the opening square bracket negates the character set e g i o 9 matches any non digit character A series of pattern elements enclosed in parentheses
71. alignment v Cost to open a gap Default v Cost to extend a gap Default v Figure 6 1 Launch page for an analysis tool which will be run interactively see also section 6 4 Interactive and Batch Tools p 140 139 140 Analysis Tools For sequence similarity searches there is usually a choice of databanks to be searched In many cases using the other default values on the Launch page should provide adequate results However the values can be changed freely should the need arise SRS will display an error message if an invalid value is given The full sequence is displayed providing the analysis tool has been accessed from a valid query rather than direct from the Tools Select page This means that you can edit it usually by changing the begin or end position Editing the contents of the sequence itself is also possible 6 4 Interactive and Batch Tools 6 4 1 Introduction When you click on the Launch button the chosen analysis tool will either be run interactively you wait for the results to be displayed or will be submitted to a batch queue The Launch page indicates which method is to be used Figure 6 1 above shows the Launch page for a tool which is to be run interactively Figure 6 4 below shows a typical batch queue message from a Launch page for a tool which has been sent to a batch queue Note The choice of whether tools are run interactively or sub mitted to batch queues depends on how SRS
72. ameters Number of hits and alignments to show 50 Filter query sequence Number of best hits from a region to keep 100 Scoring matrix BLOSUM62 v The E value 10 000000 word size Default v Perform gapped alignment v Cost to open a gap Default v Cost to extend a gap Default v Use lowercase filtering of query sequence Figure 1 22 Launch page for an interactive tool 2 Use the default parameters see step 6 above 3 Choose a view from the drop down menu unless you want to use the default view Figure 1 23 27 28 SRS Quick Tour Result Display Options View results using Blast View v Show 30 sj results per page Show results automatically v Figure 1 23 Choosing a view with which to display the results of a BLASTX analysis run interactively 4 Click the Launch button to start the tool running see Figure 1 24 LION Bioscience v LION Help Center 2 Quick Select Query Custom i Sanches Databanks Form Tools Results Projects Views Information SRS Tool is currently running Please don t go back Whenever the execution finishes the results will be presented here Tool command was srsuser rice linux_7 bin blastall p blastx d srsdata flatfiles blast swissn al lt gt mnmaccuccc Welcome to SRS 7 1 BLASTX JobName temp jobi SYAHIiKonQp RUNNING BLASTX JobName temp jobi SYAH
73. ample explains how to create a table view that can be used for SWISS PROT and for which links to EMBL should be shown 1 Click the Custom Views tab to display the View Manager page 1 On this page you can select databanks and choose a name for your customized view See Figure 1 11 Give your view a name by typing it in the View name box This example uses the name myTestView Use the Display results as options to indicate whether you want to create a table or list view In the Show fields from options indicate whether you want to be able to select fields from all of those available for your chosen databanks or only common fields In the list under Databanks to define a view for click SWISSPROT to select it In the list under Databanks to be linked to click EMBL SRS Reset Create View Options View name myTestView Display results as table C list LION Bioscience Databanks to define a view for Databanks to be linked to Show fields from C All fields in databanks Common fields only EMBL EMBL reference EMBL features EMBL counter SWISSPROT SWISSPROT_reference SWISSPROT comment SWISSPROT feature SWISSPROT counter EMBL Release EMBLRELEASE_features EMBLRELEASE_reference EMBLRELEASE_counter EMBL Updates Delete View E Names only hd EMBL reference EMBL features EMBL counter SWISSPROT SWISSPROT reference SWISSPROT comment SWISSPROT feature SWISSPROT co
74. are project work with another user Unlike permanent projects you cannot rename delete or switch between temporary projects nor can you share queries and views This means that any queries or views created for LION Bioscience one project will usually have to be recreated from scratch if you wish to use them with another temporary project The Project Manager page is described in section 2 4 Using the Project Manager p 47 2 3 Permanent Projects Permanent projects exist within SRS user accounts There are two types of account secure and non secure e A secure user account gives you an httpd password This ensures that the account and the permanent projects within it are available only to those authorized to access it e A non secure user account also uses a login procedure to identify the account that you wish to open but does not enforce any kind of access control Anyone who knows the account name can view the account and the permanent projects within it A permanent project regardless of the type of account used stores all your project data in a single location from where it can be recalled Within your user account you can swap between projects and move work from one project to another as well as retrieving saved projects e g from other accounts to which you have access or from temporary projects that have been saved Note Check with your SRS Administrator about your site pol icy for permanent projects
75. are used to tel SRS to include a 127 128 Views datafield in the results You do not have to enter a search term in a field to have it included in the results The drop down list in the Result Display Options box allows you to choose whether to create a table or list view P LION Help Center 2 Select Query Quick Custom Searches Databanks Form Views Information Tools Results Projects SRS Reset search SWISSPROT Search Options Fields you can search Your search terms Create a view In a single field you can separate multiple values by amp m Search Combine search terms amp AND AllText amylase with ID Iv Use wildcards M Accession Number Iv Get results of type Primary Accession Number O Entry Description O Result Display Options Gene Name v yword iv C View results using eywords SeqSimpleView s Entry Creation Date select gt 1 gt Jan J YYYY 1 x dan J YYY r or LastSequenceUpdate select gt Jan gt YYYY 11 v Jan v vvvv Vv Create a list x LastAnnotationUpdate select J 1 gt Jan gt YYYvY 1 v Jen gt YYYY iv view using sele table i Ad list gt Organism Name v Sequence Format Taxon r swiss NCBI TaxId lt C Show 30 z Organelle o results per page ProteinID n You can also use the Standard Query Form DbName or r C and Figure 5 17 Select the fields to include on the Extended Query Form To create a vie
76. ave it to your computer Open seve Cancel More Info IV Always ask before opening this type of file Figure 2 9 File Download dialog 4 Click _ s 5 In the Save As dialog box give the project file a name save as Save in C3 LION_SRS_Projects J ofen My Recent Documents Desktop 2x wgetzca635071 My Documents Sr My Computer o UM Emag File name TEESE Places Save as type Document Cancel VA Figure 2 10 Save As dialog Note It is better not to include spaces and other special char acters in names as some systems do not handle them prop 51 52 SRS Projects erly Use an underscore or start new words with a capital letter instead 6 Click se The file is now saved and the system is ready to save another project if you wish 2 4 5 Opening a Saved Project You can open a saved project e g from a different account to which you have access or a temporary project that was saved using the Leen button in the Other Projects box on the Project Manager page To open a project from your local disk 1 Type the file name in the text box beside the _ Browse button or use the _ Browse button to help locate your project 2 Click the 9Pen button This will open the project and you can start working with the project as usual 2 4 6 Deleting a Project When you no longer need a project you might want to delete it This may bec
77. bentries that contain only co authored papers whilst searching for the two terms using separate text boxes will produce reference subentries which contain papers by both authors but will not check whether they are co authors 76 Querying with SRS Query swissprot Authors smith amp swissprot Authors jones found 1215 next entries ROT reference 4AATM LUPAN 1 ROT reference 4MYG YEAST 2 ROT reference 4MYH YEAST 1 ROT reference 4R16 YEAST 1 ROT reference AXL2 YEAST 2 ROT reference BNR1 YEAST 1 ROT reference COPE YEAST 2 ROT reference DA81 YEAST 3 SWISSPROT reference DAL4 YEAST 2 SWISSPROT reference DBF8 YEAST 3 SWISSPROT reference DCG1 YEAST 2 SWISSPROT reference DN43 YEAST 2 SWISSPROT reference FKH1 YEAST 2 SWISS SWISS SWISS SWISS SWISS SWISS SWISS SWISS D v jo 9 U U p p o U 0000001010010000 Figure 3 14 Query Result page showing the results of a query for subentries using the References Authors subentry fields using the Standard Query Form Searching for Subentries which Reference Papers that are Co authored by Smith amp Jones using the Extended Query Form Querying subentry fields on the Extended Query Form is similar to that on the Standard Query Form However because the Extended Query Form does not allow you to search the same field using two separate text boxes it is not possible to repeat the type of search done in Searching for Entries wh
78. bentry fields searching for papers which are co authored by Smith amp Jones 4 Leave combine searches with set to amp AND and retrieve entries of type set to Entry 5 Click the Search button 73 74 Querying with SRS Query swissprot Authors smith amp swissprot Authors jones gt parent found next 1214 entries SWISSPROT Accession _Description _ SeaLength SWISSPROT AATM LUPAN Aspartate aminotransferase P2 mitochondrial P26563 precursor EC 2 6 1 1 Transaminase A 454 Fragment I SWISSPROT AMYG YEAST Glucoamylase intracellular sporulation specific P08019 EC 3 2 1 3 Glucan 1 4 alpha glucosidase 549 1 4 alpha D glucan glucohydrolase SWISSPROT AMYH YEAST Glucoamylase 1 S2 precursor EC 3 2 1 3 P08640 Glucan 1 4 alpha glucosidase 1 4 alpha D 1367 glucan glucohydrolase SWISSPROT 4R16 YEAST P40518 ARP2 3 complex 16 kDa subunit P16 ARC 154 SWISSPROT AXL2 YEAST P38928 AXL2 protein precursor SRO4 protein 823 SWISSPROT BNR1 YEAST P40450 BNI1 related protein 1 1375 SWISSPROT COPE YEAST Ip40509 Coatomer epsilon subunit Epsilon coat 296 protein Epsilon COP Figure 3 12 Query Result page showing the results of a query for entries using the References Authors subentry fields using a single text box with two search terms to search on the Standard Query Form In essence this search looks for refe
79. ded VEI Gee d ear pu des 110 5 2 USNE VIEWS Lose Sx ha o ae UR PATROL ew EUR RU 110 How to Apply Views ive RR Re IR BR RUE 111 5 3 Creatine VIEWS ok ees tr A aaa i Oa eter eng ET 123 Creating Views from the Query Forms 04 124 Creating Views using the View Manager Pages 129 CHAPTER 6 ANALYSIS TOOLS o s ens raeo kho PES a VE RE EX URP VERE SELENE OO ER 137 CHAPTER 7 COMMAND LINE SRS 54 ro e eR e oh A Rn ERO EE 149 PN OBEBE aV A TES quc dies fedus d d m qudm 150 SAG CM 151 CHAPTERS SRS QUERY LANGUAGE 55 65 65 6 56 RR ERA VERTS ERO CE RR CESAR EN eee eS RE 155 OL JntrOdU CHO asco e eL AR e USE Pel RE ERE 156 5 2 Searchin in Indices os eos DIS REPE RE 157 Introduction coe sb opie Dares bh eres per PUES 157 General Syntax 7 4 ege saws eds oat Swe DU aae Ae ends 157 Search S ECTRES avs once Ou Rua es 9 hU ee Be gt dee E RO gene SPUR S is 158 LION Bioscience Searching Using Numerical Ranges 2 04 161 Searching for Datesa ctus vett ERR e ERE Pd 163 Searching Multiple Databanks llle 164 8 3 Combining Search s ss voex es gx ER Ra e EX ERES 165 EntroduellOD e uer Sex Lope se vent eS ex uns at trcs eot 165 General Syntax ous seks o LA cred Me CE E 165 Operands sar ales sed enda eT tL A se a acd 167 Operators eae ada RES SAO ORE DAS RE E E AGIR heh AGE 168 Use of Operators to Combine Search Items 171 8 4 Entries and Subentries Was oe doe o
80. earch methods are detailed later in this chapter see section 3 2 Quick Searches p 60 section 3 3 Query Forms p 62 section 3 5 Expression Queries p 79 and section 3 7 Browse Index p 86 3 1 1 Single Word Searches When you search a databank for a single word such as reductase in a single field the results of your query will be a list of entries that included that word in the index for the selected datafield LION Bioscience 3 1 2 Multiple Word Searches You can search for a phrase having more than one word such as aldehyde reductase in several ways For example if the phrase is enclosed in quotation marks aldehyde reductase SRS will search for the complete string only returning exact matches If the phrase is not enclosed in quotation marks aldehyde reductase SRS will search for each word separately combining the results in some fashion The default is to require an entry to contain each of the words in the phrase so that a search for aldehyde reductase without quotation marks would find entries that have either aldehyde and reductase or the complete string aldehyde reductase You can make the relationship between the words explicit by including an operator in the string see section 8 3 4 Operators p 168 For example you could search for aldehyde amp reductase AND or aldehyde reductase OR or aldehyde reductase BUTNOT 3 1 3 Numbers and Dates SRS uses numerical
81. ed select J 1 j Jan j YYYY 1 z Jan Y Y YY Sequence Length gt x lt BE GE E Ea of Tb BE D Figure 3 6 Part of the Extended Query Form 1 From the Select Databanks To Search page select the databank s you wish to search by ticking the check box es to the left of the databank name s 2 Select Extended Query Forn button from the Search Options box This will display the Extended Query Form 3 Enter the search phrase s see section 3 1 Search Terms p 56 in the text boxes beside the relevant fields LION Bioscience Note You do not have to complete all the fields but the greater the detail the more refined your search will be 4 Use Combine search terms with drop down list to spec ify the method by which the various search terms should be combined amp AND OR or BUTNOT Choose the type of entries you wish to retrieve using the Get results of type drop down list Leave it set at Entry for this example Choose a view using the View results using drop down list or choose Create a view See chapter 5 Views p 109 for more information on views Choose the Sequence format using the drop down menu Specify the number of entries to display per page using the drop down list Click the Search button Description histamine v Keywords 77770000 v Organism Name man ss ss sSSSSSSSSSCS r Taxon r Organelle CT O Comment 2 1 r Entry Creation Date
82. entries Output To 9 Browser Window HTML O File text Save As ASCII text table Save with view Complete entries v Column Separator Record Separator t n O Generic XML format Using the loader seqsimple v O O Specific XML format Using the loader seqsimple v Using XML PrintMetaphors with id no valid metaphors found M Save Figure 1 28 Set the save options on the Save Options page 5 Click the 5ave 7 button Your browser s File Download dialog box Figure 1 29 will be displayed 33 34 SRS Quick Tour File Download x 9 Some files can harm your computer If the file information below E looks suspicious or you do not fully trust the source do not open or save this file File name wgetzca535071 File type From mallard Would you like to open the file or save it to your computer Open L sme Cancel More Info IV Always ask before opening this type of file Figure 1 29 The File Download dialog box Note Dialog boxes shown throughout this User Guide were generated in the WindowsNT version of Internet Explorer 5 The dialog box you see may look different depending on your system and web browser 6 Click the Se button This will display the Save As dialog box 2x My Recent Documents Desktop 9 My Documents t gr My Computer My Network File name AEREE Places Save as type Document Cancel 7A Figure 1 30
83. eroid delta isomerase EC 5 5 3 3 1 Delta 5 3 ketosteroid isomerase Figure 1 3 The results of your query shown on a Query Result page Note If you want to look at a complete entry click on its hyperlink You can sort your results to help you find the ones you are most interested in See Sorting Results p 10 for more information on how to do this LION Bioscience The next section will take you through making a query using the Standard Query Form 1 3 2 Making a Query Using the Standard Query Form See Querying with SRS This example will take you through making a query which Chapter 3 for more uses the SRS Standard Query Form to search for the word mormation kinase in the Description field of the SWISS PROT databank Before you start your query you must choose the databank s in which you wish to search To do this you have to use the Select Databanks to Search page 1 Click the Select Databanks tab 2 On the Select Databanks to Search page select the SWISS PROT databank by ticking the check box to the left of the SWISSPROT hyperlink SRS Quick Tour SRS Release 7 1 amp LION Quick Searches Help Center Select uer Databanks baat Tools f Results f Projects Custom Views Information SRS Reset Quick Search Search Options Available Databanks Expand all Collapse all Show databanks tooltips 1 Select the databa
84. erview 10 using expression queries 80 query forms 62 extended 65 standard 8 62 query language 155 179 180 operands 167 operators 168 linking 169 logical 169 regular expressions 159 search combining 165 dates 163 index 157 multiple databanks 164 numerical ranges 161 syntax 165 what is it 156 wildcards 159 query manager page 17 20 linking from 99 query result page 5 10 linking from 101 quick search 60 using 61 R range search 157 ranges combining 163 numbers and dates 57 regular expressions 59 examples 161 query language 159 rename 53 results sorting 82 overview 10 S save 33 50 save as dialog 34 search dates query language 163 index query language 157 numerical ranges query language 161 query language dates 163 index 157 numerical ranges 161 quick search 60 using 61 strings query language 158 terms 56 dates 57 multiple word 57 numbers 57 regular expressions 59 single word 56 wildcards 59 secure permanent projects 43 starting 44 select application select page 21 sets 176 single word search terms 56 Sort results 82 overview 10 spaces databank group names 164 filenames 35 51 53 131 passwords 44 usernames 44 special characters databank group names 164 filenames 35 51 53 131 passwords 44 usernames 44 standard query form 8 62 start permanent projects 44 project 39 start page 39 temporary projects 41 start page 2 string search query language 158 string search 157
85. esult of the above sort is shown in Figure 3 24 Query swissprot Description kinase found 3741 entries next SWISSPROT ABL MLvAB PO0521 protein kinase V ABL Abelson murine ure ReddyEP P EE transforming protein virus Smith M J ABL EC 2 7 1 112 Srinivasan A Groffen J Heisterkamp N Reynolds F H Jr Stephenson J R SWISSPROT KKA6 ACIBA P09885 Aminoglycoside 3 APHA 6 Acinetobacter baumannii Martin P phosphotransferase Jullien E EC 2 7 1 95 Courvalin P Kanamycin kinase type VI Neomycin kanamycin phosphotransferase type VI APH 3 VI SWISSPROT PPK Acipa Q9X4M8 Polyphosphate kinase PPK Acinetobacter baumannii Gavigan J A EC 2 7 4 1 Marshall L M Polyphosphoric acid Dobson A D W kinase ATP polyphosphate phosphotransferase SWISSPROT PTK ACIDO 052788 Tyrosine protein kinase PTK Acinetobacter johnsonii Grangeasse C ptk EC 2 7 1 112 Doublet P Vaganay E Vincent C Deleage G Duclos B Cozzone A J Riberty M Querying with SRS Figure 3 24 Query Result page showing the results from a search of the SWISS PROT Description field for the word kinase sorted according to the Organism Name field and displayed using the SwissView view 3 7 Browse Index 3 7 1 About Browsing Indices In addition to the other search methods you can also browse the indices for a search term 3 7 2 Browsing Indices You can browse indices from t
86. ew created in section 1 6 1 Creating a View p 14 but can equally refer to any other view in the drop down list 1 Click the Results tab to get to the Manage your Query Results page Choose a set of results that you wish to view e g by tick ing the check box beside them on the Manage your Query Results page See Figure 1 13 Tick the check box beside the query labelled Q1 This was the first query you made hence Q1 Select myTestView from the drop down list in the Results Display Options box 17 18 SRS Quick Tour P LION Help Center Quick Select Custom Searches Databanks Results Projects Views Information Reset Search using a query expression a Results Options Options are applied to selected queries only 4 x m Search Result History Save results Save Name Type Total No From No Query Expression Comment Delete results Delete Qa link 2 EMBL 6 SVISSPROT ID ISPE 4 Combine queries O Q3 select 1 SWISSPROT 1 SWISSPROT ID ISPE_Z with amp AND 4 b Combi JASE T Q2 query 3741 SWISSPROT 3741 tswissprot Descripti Find related info Link Voi workflow 3987 SWISSPROT 3987 rewrssPROT alltext d Results Display Options d View results using Complete entries default view Names only Complete entries SeqSimpleview FastaSeqs SwissView proteinChart myTestView Figure 1 13 View a set of results using your own v
87. ext fields in an entry you cannot control the field within which the search text occurs 1 From the Select Databanks To Search page select a databank to search e g SWISS PROT 2 Enter smith amp jones in the Quick Search text box 3 Click the Quick Search button smith amp jones Quick Search Available Databanks Expand all Collapse all Show databanks tooltips IV EMBOSS Results Sequence databanks complete alll M EMBL V SWISSPROT Sequence databanks subsections l Tool Results Figure 3 17 Quick Search of SWISS PROT for smith amp jones In this case you cannot tell SRS that you want only to search the subentries and you have no way of indicating that you wish to search only for papers that are co authored by Smith amp Jones The results will be entries which contain papers by both authors without any control over whether the papers are co authored The same results could be achieved using the Alltext fields in either the Standard or Extended Query Forms LION Bioscience Query swissprot ALLTEXT smith amp swissprot ALLTEXT jones found 1336 entries next SWISSPROT ETT BEEN ON NN SeqLength SWISSPROT AATM LUPAN Aspartate aminotransferase P2 mitochondrial SWISSPROT COPE YEAST p40509 protein Epsilon COP P26563 precursor EC 2 6 1 1 Transaminase 454 Fragment I SWISSPROT AMYG YEAST Glucoamylase in
88. ext to the entry for which you want to find related items 2 Click the Link button in the Result Options box to dis play the LINK page 11 12 SRS Quick Tour Ud LION Help Center 7 nag inec iue Tools Results Projects usnm Information SRS Reset Find entries related to current query SWISSPROT ID 1433 OENHO in other databanks Link Options Databanks Available to Link to Expand all Collapse all Select the databanks you want to search for related information To Parent Entry Find related entries EMBOSS Results Refine Query show i Sequence databanks complete v only results with all 7 EMBL SWISSPROT related entries Show only results without related entries l Sequence databanks subsections l Tool Results O m _Search Display Options Show 30 results per page SRS Release 7 1 Copyright 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 1 8 LINK page 3 Tick the check box to the left of the databank in which you wish to find links e g EMBL 4 Click the Search button to search for the related results The result will be a list of all the EMBL entries that are related to the SWISS PROT entry or entries with which you started These will be displayed on the Query Result page SRS Reset Query SWISSPROT ID ISPE ZYMMO gt EMBL found 6 entries EMBL ECAPH Apply Options to EMBL ECT903
89. f steps from selecting the databanks to viewing the results 1 Tick the check box es to the left of the databank s you wish to search on the Select Databanks To Search page 2 Enter the search term in the text box beside the Quick Search button Use a suitable word or expression see section 3 1 Search Terms p 56 3 Click the Quick Search button 61 Querying with SRS Jamylase Quick Sea ye Available Databanks Quick Search Expand all Collapse all Show databanks tooltips v l EMBOSS Results l Sequence databanks complete al EMBL M SWISSPROT Sequence databanks subsections l Tool Results Figure 3 3 Quick Search of the SWISS PROT databank for amylase 3 3 Query Forms 3 3 1 About Query Forms Results of queries can usually be refined by adding to the information used for the search If you are able to supply a larger range of information about your area of interest then SRS can target your query more precisely The query forms allow you to enter specified information about your subject in various fields There are two types of query form the Standard Query Form and Extended Query Form These are described in the remainder of this section 3 3 2 Using the Standard Query Form The Standard Query Form allows you to enter up to four separate search terms and search against up to four different datafields simultaneously LION Bioscience a LION Help Center Quick
90. h SWISSPROT AMY1 AERHY po2630 Alpha amylase precursor EC 3 2 1 1 1 4 alpha 464 eee Pe ee D glucan glucanohydrolase SUMUS re evan cinese r1 Alpha amylase 1 EC 3 2 1 1 1 4 alpha D glucan SWISSPROT AMY1 DICTH R 21 7 D results Tools Er P09961 glucanohydrolase i caa i m SWISSPROT AMY1 ORYSA Alpha amylase precursor EC 3 2 1 1 1 4 alpha Linie n lE rus ee apee og a a REDI D glucan glucanohydrolase Isozyme 18 428 Link SWISSPROT AMY2 DICTH Alpha amylase 2 EC 3 2 1 1 1 4 alpha D glucan SWISS PRU AMi e VICIO P14898 hydrol 562 Save results Save glucanohydrolase SWISSPROT AMY3 DICTH Alpha amylase 3 EC 3 2 1 1 1 4 alpha D glucan rcd VATES UH P14899 glucanohydrolase d 498 Display Options SWISSPROT AMY3 HORVU Alpha amylase type B isozyme precursor EC P04747 3 2 1 1 1 4 alpha D glucan glucanohydrolase 368 Clone PHV19 Fragment View results using SWISSPROT AMYB DROME Alpha amylase B precursor EC 3 2 1 1 1 4 SeqSimpleView x POLOT alpha D glucan glucanohydrolase a93 SWISSPROT AMYR BACSS Raw starch digesting amylase precursor EC Sort results by P17692 3 2 1 1 1 4 alpha D glucan glucanohydrolase a unsorted v SWISSPROT AMYR DROPS 018552 Alpha amylase related protein precursor EC 494 3 2 1 1 9 ascending Alpha amylase related protein precursor EC O descending SWISSPROT AMYR DROSU 018420 3 2 1 1 494
91. h amp Jones jointly and those which contain separate papers by Smith and by Jones LION Bioscience A search using subentries on the other hand will allow the user to specify a relationship between the two authors i e to specify that there must be at least one reference that is written jointly Using subentries allows each literature reference to become a specific subentry in effect creating a mini entry within an entry The next section will take you through a typical subentry query 3 4 3 Querying Using Subentries This worked example will take you through using subentries to make queries using both of the Query Forms Searching for Entries which Reference Papers that include those by Smith and by Jones using the Standard Query Form In this example entries will be retrieved that reference papers by Smith and Jones For an entry to be retrieved there must be papers whose authors include Smith and Jones but Smith and Jones need not be co authors of the same paper 1 From the Select Databanks To Search page select the databank you wish to search by ticking the check box to the left of the databank name e g SWISS PROT 2 Select Standard Query Form button from the Search Options box This will display the Standard Query Form 69 Querying with SRS 3 Use the first drop down datafield list to select an appropri ate subentry field e g Reference Authors Note Datafields for subentry fields are shown in the dr
92. h have unspecified problems may be shown with aa Icon DD bid Help Center O LION va ee aes Seen tet Tools Results f Projects rom Information SRS Job Options List of Batch Jobs Job Name Status Start Date Results Result Queue Name Options are applied to from Set selected jobs only 19 Mar 2003 BLASTP Qe 1s priority m klee Delete jobs Delete temp blastp 2 15 07 batch 19 Mar View job results using 2003 BLASTN Q3 50 priority m klee temp blastn 1 14 21 batch Complete entries View Run job again with different options Edit Options SRS Release 7 1 Copyright 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 6 8 Job Status page showing multiple jobs LION Bioscience 147 6 4 3 5 Accessing the Job Status Page The H icon appears on SRS pages when batch jobs exist and can be used to access the Job Status page It changes to B4 when all jobs have completed 148 Analysis Tools CHAPTER COMMAND LINE SRS The SRS command line interface is called getz This chapter e Introduces getz e Explains the available getz options 150 Command Line SRS 7 1 getz The SRS command line is available through a UNIX shell window and uses a program called getz You may need to contact your SRS Administrator to set this up Using getz you can query databanks from the command line For further information on creating getz queries see section 7 1
93. he Field Information page for the datafield type e g Description SeqLength that interests you See section 3 7 3 Getting to the Field Information Page p 88 for more details of how to get to this page LION Quick Select Custom Searches Databanks rm Tools Results Projects SRS Field Name Description Data fields in SRS Browse Index LION Bioscience Help Center Views Information Description This is probably the best data field for searching an entry you don t know very much about however you can t expect to find all entries of a class since often different conventions are used for naming enzymes organisms genes etc Databank Name Print Name Short Name Type No of Keys No of Entry References Indexing Date Status SWISSPROT Description Description des index 0 0 see member databank List values that match F and occur in at least 1 entries List Values Figure 3 25 Field Information page for the Description field index for the SWISS PROT databank 1 Onthe Field Information page for the appropriate data bank and datafield enter your search term using wild cards as appropriate Note In contrast to other query methods implicit wildcards are not appended automatically to the search term when browsing indices and must be specified explicitly 2 Click the List values J button This will take you to the Browse Index page 87 Querying with SRS LION Help Center
94. his entry will have links to PROSITE entries that document the protein family of which acha human is a member In this case it is the family of neuronal acetylcholine receptors These items in the PROSITE databank are retrieved The next link retrieves SWISS PROT entries that are linked to the PROSITE entries i e belong to the neuronal 172 SRS Query Language acetylcholine receptor family In effect the entry acha human is being amplified to retrieve all the entries in SWISS PROT which document members of the protein family or families to which it belongs Example 8 4 Multiple linking 2 A similar technique to that used in example 8 3 Multiple linking 1 can be used to find related information in another databank to which the initial entry is not linked swissprot id gshr caeel prodom pdb The query retrieves a probable glutathione reductase whose ID is gshr caeel from SWISS PROT searches for entries in ProDom which document related proteins and then looks for links to PDB in these entries The result is a set of PDB protein structures that are homologous to the SWISS PROT entry gshr caeel Example 8 5 Complex linking This example can be thought of as being composed of two parts q swissprot swissnew des kinase q lt swissnew The first part of the query searches the description fields of the SWISS PROT and SWISSNEW databanks looking for kinase The second part of the search excludes an
95. hors smith amp swissprot Authors jones parent The text should all be on one line and the text box will scroll as you type You can scroll back to the left to check what you have written but it is often difficult to see the whole query You could try typing the query in a suitable text editor so that you can see it and then using copy and paste to insert it into the Expression Query text box B _Search 81 Querying with SRS 3 6 Sorting Results 3 6 1 What is Sorting Many queries will yield a large number of results Sometimes it is useful to be able to sort these to help you select the most relevant results You could sort by almost any of the available fields However the fields which are available for sorting will be limited to those selected for the installation of SRS that you are using In addition a few fields are not appropriate for sorting Some typical sortable fields are shown in Figure 3 20 Display Options View results using SeqsimpleView D Sort results by unsorted unsorted Primary Accession Number Description Gene Name Entry Creation Date Organism Name Organelle Sequence Length Apply Display Options Figure 3 20 Display Options box showing drop down list of sortable fields on a Query Result page 3 6 2 Sorting a Set of Results 1 First choose a set of results e g by making a search and view them on a Query Result page uick RAE Re
96. ich Reference Papers that include those by Smith and by Jones using the Standard Query Form p 69 1 From the Select Databanks To Search page select a databank to search e g SWISS PROT and go to the Extended Query Form 2 Scroll down the Extended Query Form until you find the section marked Reference subentry fields Enter smith amp jones into the Authors text box Reference subentry fields View results using E Names only Authors Title Journal valumeNo FirstPage Year MedlineID PubMedID RefPosition RefCommentCode or C and RefComment Reference subentry fields smith amp jones sss lt SsS a a LION Bioscience Reference iim Search SI sS SS x LT th E mH Figure 3 15 Part of the Extended Query Form showing a query for subentries using the References Authors fields 3 Choose whether you wish to retrieve entire entries or the Reference subentries View results using Names only Figure 3 16 Choosing whether to retrieve entire entries or the Reference subentries 4 Submit the query as usual Reference Entry Querying with SRS Searching for Subentries which Reference Papers that are Co authored by Smith amp Jones using Quick Search The quick search option will always return complete entries You can nevertheless search for entries using the subentries as search items however as Quick Search simply searches all the t
97. ich to sort the query Ascending 0 or descending sort 153 154 Command Line SRS CHAPTER SRS QUERY LANGUAGE In SRS many actions e g retrieval commands logical operations with sets obtained from previous queries links between entries from different databanks or a combination can be expressed using the SRS query language This chapter describes the language and gives examples of its use During this chapter you will learn About searching in indices The general syntax of the SRS query language About using logical and link operators About entries and subentries About storing intermediate results in sets 156 SRS Query Language 8 1 Introduction 4 LION In earlier chapters you have seen how to use the SRS Query Forms Link page etc to create a query In addition to this method you can type your query using the SRS query language There are various places where this can be done including the Quick Search text box on the Select Databanks To Search page for example The SRS query language syntax is also used internally by SRS whenever you make any query e g using the query forms linking etc so you will see examples of them on SRS pages that contain the results of any such queries e g at the top of the Query Result page Help Center Custom Views ie Information Results Projects SRS Select Databanks Reset Query swissprot AllText cyclase found 881
98. iew 4 Click the Rerun Query button to display the query result set Q1 using myTestView The entries in Q1 will be dis played using the view you selected uick TE Reset Apply Options to SWISSPROT Lo Description emt _ Description C selected results only unselected results only Result Options Launch analysis tool Blast Launch Show tools relevant to these Tools Link to related information Link Save Display Options View results using myTestView Sort results by unsorted z ascending C descending Show 30 results per page results Save results Printer friendly view T Apply Display Options Select Databanks Query SWISSPROT alltext dehydrogenase found 3987 entries Results Projects next LION Bioscience Help Center O Information SWISSPROT 124H CLOS4 12 alpha hydroxysteroid dehydrogenase EC 1 1 1 176 Fragment SWISSPROT 25KD_ SARPE Development specific 25 kDa protein EMBL SPDEVG SWISSPROT 2BHD_STREX 20 beta hydroxysteroid dehydrogenase EC 1 1 1 53 Oo OVO a SWISSPROT 3BH1 MESAU 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type I 3Beta HSD I Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomera
99. iew could be from one or more databanks For convenience views can be categorized as predefined views and project views see section 5 3 Creating Views p 123 Predefined views are the default views that are available to everybody using an SRS server Some of these are designed to work with specific databanks and will only be available when they are appropriate Project views are views that you define using the View Manager page see section 5 3 2 Creating Views using the View Manager Pages p 129 Views can be applied from any page that creates or holds a query The following list identifies the pages where views can be created or applied to data sets The Standard Query or Extended Query Forms The Query Result page which contains the results of a query LION Bioscience The Entry page which contains the details of a single entry The Manage your Query Results page The Launch page from which you can launch tools The views drop down list available on pages such as the Manage your Query Results page contains the views that are currently available see Figure 5 1 These will change according to factors such as which views are installed on your system which databank you are using and what if any views you have created in the current project Display Options View results using SeqsimpleView ne Names only Complete entries SegSimpleView per page Printer friendly
100. ific format in a small number of cases where there is no databank entry format you may have the option of using a view from the drop down views menu The use of the drop down view menu is the same as on other SRS pages see for example the section From the Query Result Page p 114 The example below describes only the first method 1 You need to be on an Entry page so start with a Query Result page and click the entry name hyperlink for one of the entries see Figure 5 6 117 118 Views SWISSPROT 2NPD NEUCR 2 nitropropane dioxygenase precursor EC 1 13 11 32 Q01284 Nitroalkane oxidase 2 NPD 378 I SWISSPROT 2NPD WILMR 2 nitropropane dioxygenase EC 1 13 11 32 Nitroalkane Q12723 oxidase 2 NPD 374 I SWISSPROT ACC3 LYCES 1 aminocyclopropane 1 carboxylate oxidase homolog F10987 Protein E8 363 rn P03875 COX1 OXIS intron 1 protein 834 r ane em P03876 Putative COX1 OXI3 intron 2 protein 789 SWISSPROT AI3M YEAST P03877 Putative COX1 OXI3 intron 3 protein 378 Figure 5 6 Click the hyperlink for an entry 2 Assuming that the current databank uses databank spe cific and text formats the Entry page will display the entry using the databank specific format see Figure 5 7 LION Reset Quick Searches LION Bioscience Help Center o gane Results Projects Information Text Entry SwissEntry Previous Entry Entry 6 of 33 from Query
101. ilenames 35 51 53 131 passwords 44 usernames 44 command line 149 copy project information 49 creating views 123 D databank group names spaces and special characters 164 databanks search multiple 164 dates in indices search for 57 query language search for 163 delete 52 dialog file download 33 save as 34 download file download dialog 33 download options page 32 E entries 173 find all entries linking 98 linking 174 entry page linking from 103 examples expression linking 107 getz 150 linking 171 172 173 regular expressions 161 expression expression linking 104 examples 107 procedure 104 177 178 expression query 79 using 80 expressions regular expressions 59 examples 161 query language 159 extended query form 65 F field information page 88 file download dialog 33 filenames spaces and special characters 35 51 53 131 forms extended query 65 query 62 standard query 8 62 G getz 149 150 arguments 151 examples 150 H how to expression linking 104 linking 95 l index browse 86 search 157 query language 157 syntax 157 information field information page 88 interactive tools 141 intermediate results storing 176 J job status page 145 L language query language 155 link page 11 linking 91 92 entries and subentries 174 examples 171 172 173 expression linking 104 examples 107 procedure 104 find all entries options 98 from entry page 103 from query manager
102. in other projects How to move temporary project work to a permanent 38 SRS Projects 2 1 Introducing Projects There are two types of project that can be used in SRS temporary and permanent These are described below 2 1 1 Temporary Projects When you use a temporary project your queries and views are stored in a temporary location They may remain available for a time after you have finished working but you should not rely on this If you bookmark the page in your web browser you should be able to return to the project until the System Administrator clears the files You should use a temporary project for Simple searches For example a temporary project is use ful if you want to look something up quickly or run an occa sional BLAST search To find out more about running a temporary project see section 2 2 Temporary Projects p 41 2 1 2 Permanent Projects Permanent projects are used within a permanent SRS user account There may be one or more up to 99 projects within any such account All your queries and views are stored in a project or projects The fact that the projects are part of a user account means that they remain available for you to use in LION Bioscience the future whenever you choose to return to that user account User accounts and the permanent projects within them can also be password protected allowing you to restrict access You should work in a permanent project if any
103. jct 109 DVPGASGTGRARVTLGLDOPGCELHPAKDLEEEAPVRSDSEMSASVSGDHSPRGEDDSVT 168 homolog 1 Query 1190 PGAAGTTVGATTATPGSEDUKAGAESPEKKPAC RKKKTRTVFSRSQVFOLESTFDMK 1360 PG A A G AG E PA REK R FS QVF LE F Sbjct 169 PGGARVPGLRGAAGSGASGGQAGGVEEEEEPAAPKPRKKRSRAAFSHAQVFELERRFNHQ 228 BLASTX temp jobi swissnew 3 HK32 HUMAN 99 Frame 42 Homeobox 333 protein NKX 3 2 Bagpipe Query 1106 KELDSKSPDEIILEESDSEEGKKEGEAV PGAAGTTVGATTATPGSEDWKAGAESPEKKP 1282 Homaobox E 5 E s E VP 2 4 G AG E P protein Sbjct 140 EEAAGRSDSEMSASVSGDRSPRTEDDGVGPRGAHVSALCSGAGGGGGSGPAGVAEEEEEP 199 homolog 1 Query 1283 AC RKKKTRTVFSRSQVFQLESTFDMKRYLSSSERAGLAASLHLTETQVKIWFQNRRN 1453 n REK R FS QVF LE F RYLS ERA LAASL LTETOVKIWFONRR Sbjct 200 AAPKPRKKRSRAAFSHAQVFELERRFNHORYLSGPERADLAASLKLTETOVKIWFONRRY 259 x BLASTX temp jobi swissnew 4 HM1D DROAN 92 Frame 42 Homeobox 606 protein OM 1D Query 1097 PDHKELDSKSPDEIILEESDSEEGKKEGEAVPGAAGTTVGATTATPGSED WKAGAE 1264 P ELD E DS EG G G G H K G Sbjct 262 PAGAELDDSSDYHEENEDCDSDEGGSAGGGGGGSNHMDDHSVCSNGGKDDDGNSIKSGST 321 Query 1265 SPEKKPACRKKKTRTVFSRSOVF OLESTFDMKRYLSSSERAGLAASLHLTETOVKIUFON 1444 s K RT F Q LE F YL3 ER LA L L OWK UON Sbjct 322 SDMSGLSKKQRKARTAFTDHQLQTLEKSFEROKYLSVQERQELAHKLDLSDCQVKTWYON 381 v Figure 1 26 Part of a Query Result page showing one of the pre defined SRS views 1 8 Saving your Results See section Temporary 1 SRS allows you to save queries so you can
104. lt Q2 amp Q3 In Q1 that link to Q2 and Q3 lt Q1 Q2 Q3 In Q1 that link to Q2 or Q3 Q1 Q2 Q3 In Q1 that link to Q2 but not Q3 LION Bioscience 107 4 5 3 Expression Linking Examples If you have a set of EMBL entries in a query Q3 which you wish to search for links with the SWISS PROT databank type Q3 lt swissprot This will show the EMBL entries from the original query that have links to the SWISS PROT databank If you would rather see the SWISS PROT entries that the above operation returned turn the linking operator around so that it points towards SWISS PROT Q3 gt swissprot ofl This returns the SWISS PROT entries that have links with the entries in Q3 108 Links to Additional Data CHAPTER VIEWS SRS includes a number of predefined views that you can use to change the way in which your results are displayed In addition you can create your own views During this chapter you will learn About the predefined views available in SRS How to work with views How to create and use your own views 110 Views 5 1 What is a View 5 2 Using Views SRS uses views to determine which data types are shown A view may include only a few data types or it may display all available types of data In addition to the predefined views which are part of SRS you can create your own views A view can be defined to work with a specific databank or with several databanks The data in a v
105. lta 5 gt 4 isomerase type I 3Beta HSD I Includes 3 beta p22071 hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 372 I 3 beta hydroxy 5 ene steroid dehydrogenase Display Options Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase View results using SWISSPROT 3BH MESAU 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 SeaSimpleVi isomerase type II 3Beta HSD II Includes 3 beta enomp Enon 64421 hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 372 Q I 3 beta hydroxy 5 ene steroid dehydrogenase Sort results by Progesterone reductase Steroid delta isomerase EC unsorted 5 3 3 1 Delta 5 3 ketosteroid isomerase O SWISSPROT 3BH2 MOUSE 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 amp ascending LIEN eee M E ee isomerase type II 3Beta HSD II Includes 3 beta C descending p26149 hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 265 I 3 beta hydroxy 5 ene steroid dehydrogenase l z I Progesterone reductase Steroid delta isomerase EC stile TERM MISSUS 5 3 3 1 Delta 5 3 ketosteroid isomerase Fragment de I SWISSPROT 3BH2 RAT 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 3 4 3 REISEN Cw ee isomerase type II 3Beta HSD II Includes 3 beta Printer friendly view T See hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 Bs 3 3 beta hydroxy 5 ene steroid dehydrogenase Apply Display Options Progesterone reductase St
106. med that you have arrived at the Link page Figure 4 4 Use section 4 4 Getting to the Link Page p 99 to help you navigate here if necessary 95 96 Links to Additional Data Ud LION Help Center 7 ECKE RC d uey Tools Results f Projects on Information SRS Reset Find entries related to current query EMBL ID 421640 in other databanks Link Options Databanks Available to Link to Expand all Collapse all Select the databanks you want to search for related information To Parent Entry Find related entries EMBOSS Results Sequence databanks complete Refine Query show only results with alij EMBL SWISSPROT related entries Sequence databanks subsections Show only results SeqRelated without related entries Tool Results mb Search Display Options Show 30 results per page Figure 4 4 The Link page for linking initiated from the Manage your Query Results and Query Result pages Note There are two forms of the Link page If you have initi ated the links from either the Manage your Query Results or Query Result pages then you will see the Link page as shown in Figure 4 4 If you have initiated linking from the Entry page then the Link Options are not available see Figure 4 5 LION Bioscience Pd LION Help Center sneer EIAS Ruery Tools Results f Projects oon Information SRS Reset Find entries related to EM
107. metimes the predefined SRS views may not show the information that you want to see To allow you to view the particular information you require you can create your own views using the View Manager page or from the Standard 123 124 Views Query Form or Extended Query Form These are referred to as project views 5 3 1 Creating Views from the Query Forms Both the Standard Query Form and the Extended Query Form provide a mechanism for specifying the datafields to be displayed on the Query Result page that results from the current query This section describes how this is done Creating Views from the Standard Query Form The bottom half of the Standard Query Form has a section entitled Create a view which allows you to specify the datafields that are to be used to display the results of your query see Figure 5 12 You can also choose whether to display the results using a table or a list view and the sequence format that is used Create a view Select the fields you want displayed in your view and choose the format Choose 1 or more fields Display As Table C List Accession Number 1 i Sequence Format swiss X Primary Accession Number Description Gene Name Entry Creation Date ium Search Figure 5 12 Specifying the datafields to be used to display results on the Standard Query Form To design your own view LION Bioscience 1 Select the datafields you want to display from the Choose 1 or mo
108. nks you want to search EMBOSS Results 2 Enter your search terms in the Quick Search box or choose a query form from below Standard Query Form Extended Query Form You can browse through all the entries in any databanks First select the databanks you want to browse then click Browse Entries gt bookmark this link to return to your project Sequence databanks complete aii EMBL v SWISSPROT Sequence databanks subsections ali EMBL Release EMBL Updates SWISSPROT Release SWISSPROT Updates Tool Results ali BLASTP BLASTN BLASTX TBLASTN TBLASTX CLUSTALW NCLUST ALW PROSITESEARCH RESTRICTIONMAP HMMBUILD Copyright amp 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 1 4 The Select Databanks to Search page with the SWISS PROT databank selected Note This page can be reached at any time from within SRS by clicking on the Select Databanks tab 3 Click the Standard Query Forn button to display the Stan dard Query Form From here you can search databanks in many different ways amp LION Quick LION Bioscience Select Help Center Searches SRS Reset search SWISSPROT Databanks Results Projects Information Search Options Fields you can search Your search terms Combine search terms with amp AND
109. o Another Project 0 0 0 0 eee eee ee eee 48 Copying Project Information 0 0000 eee eee 49 saving d PEO COR sad etur ee ae funk rte CREA ee 50 Opening a Saved Project Gin doe t who dated Rew peewee ED 52 Deleting d Project sieden peen PER a els 52 Renanins a Project 3 egea ai vrac Eee d li ea 53 CHAPTER 3 QUERYING WITH SRS 6366 esee Fu ehh mnn ot xh ks 9 n be weeds We we Ewe eR Dn 55 S Search Terms es ve eam an oe eT s ALIE us daban 56 Single Word Searches ox ess sua Sx ore dA Ga eate ds 56 Multiple Word Searches tese ER EXE saan 57 Numbers and Dates 22 2 co8vb bacewhiveadeokebracaws 57 Regular Expressions ied aay oes Ad rS ER ER 59 bine P E 59 322 Quick Searches id ev Due UR e me E WE 60 SRS Quick Searc Page cos qouerge tatai OE ewe vee hae 60 About Quick Search llle 60 Using Quick Search 23 mro ou Ie bare wie eco eee INR SOLER 61 LION Bioscience 3 3 Query Forms oo cp pe aoe ean SG ae Aaa eee te aes 62 About Query Forms c rk der rec eee heed seks Ree 62 Using the Standard Query Form 00000 5 62 Using the Extended Query Form 00 000 5 65 DA Subentries se oue Sex verit cu Dc voten Ct Does 68 About SIDe ET S eos eros e MAL arcet s CM T s 68 Kise oF SUDEHttles i5 ia iei eod s stas ta case e eus 68 Querying Using Subentries 0 0 0 0 cee eee eee 69 3 9 Expression Queries ish se ARR baw ed nee PR E EEEAR ES 79
110. o link complete query sets using expression linking 1 Type in the name of the query set to be linked Q1 the type of query e g lt or gt see section 4 5 2 Linking Operators p 105 for more details and the databank or second query Q2 to which the set should link For instance Q1 Q2 a Y Will list all the entries in Q1 that are linked to Q2 Q1 gt Q2 a will list all the entries in Q2 that are linked to Q1 See the section 4 5 2 Linking Operators p 105 2 Click the Search button 4 5 2 Linking Operators Expression linking uses linking operators to describe the nature of the links between the specified queries or 106 Links to Additional Data databanks Typical operators are the lt and gt which indicate a link lt Entries in the set or databank to the left of the operator are returned if they have a link to any entries in the set or databank to the right of the operator gt Entries in the set or databank to the right of the operator are returned if they have a link to any entries in the set or databank to the left of the operator You can combine linking lt and gt and logical amp and Operators to build up more complex queries see the examples in Table 4 1 Table 4 1 Linking operations Operators Example Returns Entries in Q1 Q2 In Q1 that link to Q2 gt Q1 gt Q2 In Q2 that link to Q1 lt amp Q1
111. of the following apply You or a colleague will want to return to a project at a later time You want to be able to move your work from one project to another You want to keep a safe record of all your projects e You want to recall any of your previous permanent or saved projects To find out more about running a permanent project see section 2 3 Permanent Projects p 48 2 1 3 Starting a Project Whether you decide to use a temporary project or a permanent project you will begin your project from the Start page see Figure 2 1 39 40 SRS Projects ot Help Center O LION A m uet pery Tools Results f Projects FELN Information SRS Start a Permanent Project Quick Text Search Search Tips Want to know more about Searches Databanks EMBL Search using SRS go to the Help Center where you ll find all the Sequence Similarity Homology Search Search Tips searchable online help you need Get Protein Sequences v Problems with SRS please email the SRS administrator Searches Databanks Swissprot m _ Search SRS Release 7 1 Copyright 1997 2003 LION bioscience AG All Rights Reserved Terms of Use Feedback Figure 2 1 The Start page The Start page contains links that allow you to start a permanent project do a quick search if you have the relevant databanks installed on your installation or access the online help files You can also start a temporary project from he
112. ome necessary if the number of projects for a particular permanent project account nears 99 The upper LION Bioscience limit for the number of projects available to a permanent project account is 99 Note This feature is not available for temporary projects To delete a project 1 Set the project that you want to delete as the current project See section 2 4 2 Switching to Another Project p 48 2 Click the Pelete J button 2 4 7 Renaming a Project Default project names project1 project2 projectN can be personalized to make it easier to keep track of the work you have performed in each project Note This feature is not available for temporary projects To rename a project 1 Type a new name in the Rename project text box in the Project Options box Note It is better not to include spaces and other special char acters in names as some systems do not handle them prop erly Use an underscore or start new words with a capital letter instead 2 Click the Renane button The page will be refreshed showing the new project name 53 SRS Projects 9 LION Help Center ee eens Results Projects narom Information SRS Reset Contents of project2 Queries d Name Query Expression Name Account Name helenp Session project2 I Q2 swissprot FtKey transit gt parent SwissProt View projectz Options M Q1 embl FtKey transit peptide gt parent I Embl view Save to desktop Sa
113. on 8 3 3 Operands p 167 and operators see section 8 3 4 Operators p 168 Queries using the SRS query language take the general form operand operator operand See section 8 3 3 Operands p 167 and section 8 3 4 Operators p 168 for more information on operands and operators respectively For example enzyme gt pdb where enzyme and pdb are operands specifying the databanks Enzyme and PDB respectively and gt is an operator telling SRS to search for links between the databanks and keep only those entries which belong to the databank on the right The result of this query is a list of 165 166 SRS Query Language entries in the PDB databank that have links to the Enzyme databank Combinations may also include index searches For instance swissprot des kinase gt pdb will create a list of all the entries in the PDB databank that have links to the results of the index search swissprot des kinase See section 8 2 Searching in Indices p 157 for an explanation of this sub search The above examples are fairly trivial but the SRS query language allows you to build up more complex queries using the various operators In addition expressions can be grouped using parentheses so that they are treated as a single entity You will see examples of searches and ways of combining them throughout this chapter 8 3 3 Operands LION Bioscience Operands are the items upon
114. ooks for links from the subentries to their respective parent entries and retrieves a set containing parent entries For example swissprot ftkey transmem parent retrieves the parent entries the entries to which the subentries belong for the set of subentries from SWISS PROT that have transmembrane sequence features Logical operators can then be used to combine the set of parent entries with another set of entries Furthermore as with other SRS query language commands it is possible to combine the link to the parent entries and the subsequent operations into the same command see section More Complex Links using the Parent Operand p 175 More Complex Links using the Parent Operand The command swissprot ftkey transmem gt parent swissprot key transmembrane returns all entries that have the keyword transmembrane or that have transmem sequence features The index search swissprot ftkey transmem results in a set of subentries whereas the index search swissprot key transmembrane 175 176 SRS Query Language returns a set of entries These sets cannot be combined directly using a logical operator Instead an extra step must be added which finds the set of parent entries to which the subentries belong The resultant set of parent entries can then be combined with the set from the second index search using a logical operator This type of search may be necessary to ensure all entries with a certain
115. op down lists using a special format to identify them In many cases they are the same as for SWISS PROT i e a subentry name e g Reference followed by a field within that subentry e g Authors the two parts are separated by a colon Hence Reference Authors will search for authors fields within subentries 4 Enter smith in the first text box beside where you selected Reference Authors The search is case insensi tive so it does not matter whether smith is written with a lower or upper case S 5 Repeat the process for the next line of information using the name jones rather than smith Reset search SWISSPROT Search Options Fields you can search Your search terms In a single field you can separate multiple values by amp m Search Combine search terms with amp AND X e Reference Authors v smith N Reference Authors j jones AiTex E Get results of type AiTex ba Entry Figure 3 8 Standard Query Form showing a query for entries using the References Authors subentry fields 6 Leave Combine searches with set to amp AND 7 Leave Get entries of type set to Entry This will cause entire entries to be retrieved Setting this option to one of the other subentry fields e g Reference will tell SRS to LION Bioscience retrieve each reference which fulfils the search criteria as a separate entity 8 Click the Search button
116. ple Databanks As well as allowing you to search a field of a single databank the SRS query language allows you to search multiple databanks in a single query expression This is done using a list of databank names enclosed in curly brackets to replace the single databank name seen in earlier examples The names in the list must be separated by spaces For example swissprot swissnew sptrembl des kinase searches for the word kinase in the Description index of the SWISS PROT SWISSNEW and SPtrEMBL databanks It is often convenient to give a name to a group of databanks so that that name can be used later in the query rather than repeating the list of names For instance dbs swissprot swissnew sptrembl des kinase amp dbs org human creates the group dbs which combines the three databanks SWISS PROT SWISSNEW and SPtrEMBL and then uses the group name dbs to replace the search name in the second part of the search Note lt is better not to include spaces and other special char acters in names as some systems do not handle them prop erly Use an underscore or start new words with a capital letter instead LION Bioscience 8 3 Combining Searches 8 3 1 8 3 2 General Syntax Introduction The earlier parts of this chapter dealt with simple index searches The SRS query language can also be used to create more complex queries These take the form of expressions and are constructed using operands see secti
117. query 1728 SWISSPROT l Q7 select 1 SWISSPROT Ll Q4 link 6 EMBL I Q3 select 1 SWISSPROT F o2 query 3741 SWISSPROT voi workflow 3987 SWISSPROT No Query Expression Comment iN EULZUEUEEND 4 1 SVISSPROT ID 12AH C 4 b 6 SWISSPROT ID ISPE 4 La 1 SWISSPROT ID ISPE Z 4 gt 3741 swissprot Descripti 4 3987 SWISSPROT alltext d 4 Figure 5 9 Selecting the required view 3 Click the Rerun Query button Applying a View From the Launch Page for Interactive Tools Note For analysis tools run via a batch queue the option to set a view is not available on the Launch page but you can 121 122 Views apply a view to the results after they have been generated Follow the instructions given in sections From the Query Result Page p 114 and Applying a View From the Entry Page p 117 To choose a view for the results of a tool other than the default view 1 From the Query Result page choose the entries against which you want to run the tool or choose unselected only from the Apply Options to box Apply Options to C selected results only unselected results only Figure 5 10 Using the option buttons to choose unselected only 2 Select an analysis tool from the Result Options box Click the Launch button to display the Launch page See chapter 6 Analysis Tools p 137 for more informa tion on launching tools 3 Find and select the view you want f
118. re FtKey FtLength FtDescription Fields of subentry Counter CountedItem CountedN ProteinID Gene Sequence gcg z Fields of subentry Counters Use view to display entries EMBL O ID Division AccNumber D PrimAccNumber Segversion Molecule M Description Keywords Organism Taxon Organelle Comment DateCreated LastUpdated SegLength Link Sequence feste v Fields of subentry References O ID Authors Title Journal volumeNo FirstPage Year MedlineID PubMedID RefPosition Fields of subentry Features I ID AccNumber FtKey FtQualifier FtDescription FtLength FL ID Counteditem CountedN Use explicit link none Display only number of linked entries only r Datafields from databanks to be linked to Igi Save New View Figure 1 12 View Manager page 2 LION Bioscience 9 Click the Save in the Create View Options box to save your view Your view will be saved and you will be returned to the View Manager page 1 where you can create more views Your saved views will be added to the drop down list in the Results Display Options box and can be applied to your results in the same way that any other view is applied see section 1 6 2 Applying a View p 17 1 6 2 Applying a View This section demonstrates how to apply a view to your results The example uses the vi
119. re simply by using the quick search options or clicking on any of the tabs If you choose to start a permanent project you can return to projects in an existing account or open a new account There are also links which allow you to Look up the SRS on line documentation that is available on your server Contact your SRS Administrator LION Bioscience The SRS on line documentation consists of HTML and PDF versions of the available documentation This includes this User Guide and online page by page SRS help the SRS Online Guide as well as documents designed to help SRS Administrators e g the SRS Administrator s Guide the Icarus Guide Icarus Quick Reference Classes amp Commands etc 2 2 Temporary Projects Temporary projects should only be used for temporary work Temporary project data will be removed whenever your System Administrator performs a routine clean up operation 2 2 1 Starting a Temporary Project A temporary project is started from the Start page By default a temporary project will be started for you as soon as you start to perform tasks within SRS 1 For example click on the Quick Searches tab This takes you to the SRS Quick Search page You will see the temporary project ID in the place where the option of starting a permanent project appeared on the Start page Temporary Project SY amp GnikKmno3 Figure 2 2 Typical temporary project ID as shown on the SRS Quick Search page 42
120. re Info Figure 1 16 Tool Select page Note You can also access many of the most commonly used tools using the drop down list in the Result Options box Selecting the tool from the drop down list and pressing the Launch button takes you directly to the Launch page see step 4 4 f you have selected a query for which BlastN is available then click on the Launch hyperlink for BlastN Similarity Search Tools BlastP BLASTP Protein Protein Sequence Similarity Search Launch More Info BlastX Sequence Similarity Search Launch More Info BlastN Sequence Similarity Search Launch More Info TBlastX Sequence Similarity Search Launch More Info TBlastN Sequence Similarity Search Launch More Info HmmBuild Search a sequence for matches to profiles Launch More Info Figure 1 17 Selecting BlastN 5 This will take you to the Launch page If BlastN is not available then try again with another LION Bioscience query or select one of the other tools that is available not ing that the images below refer to BLASTN and will be slightly different for your case SRS Aun BlastN More Info iexeqga pre Job name Database to search temp EMBL Updates m Launch Note this tool is run by LSF batch queueing system Select a queue to submit jobs to blast m sisley batch Parameter set options Save current parameter set or enter file name Browse Strand of
121. re fields list see Figure 5 12 Note You can usually use the Shift or Control keys to select multiple fields but refer to your browser s documentation for help if required 2 Choose whether you wish to display the results using a table or a list view using the option buttons Display As Table List Figure 5 13 Table and list view option buttons 3 Choose the sequence format using the drop down list Sequence Format swiss Figure 5 14 Sequence format drop down list 4 Complete the query as normal The results will be displayed on the Query Result page as specified 125 126 Views Help Center Quick Select Searches Databanks Projects 5 Information SRS Reset Query swissprot ALLTEXT amylase found 99 entries next Apply Options to SWISSPROT accession __Description pha amylase isozyme 3D precursor EC 3 2 1 1 b SWISSPROT AM3D ORYSA 3 aoe P27933 1 4 alpha D glucan glucanohydrolase 435 SWISSPROT AM3E ORYSA Alpha amylase isozyme 3E precursor EC 3 2 1 1 9 unselected results only P27934 1 4 alpha D glucan glucanohydrolase 437 SWISSPROT AMC1 ORYSA Alpha amylase isozyme C precursor EC 3 2 1 1 Result Options P27940 1 4 alpha D glucan glucanohydrolase Isozyme 383 1B i SWISSPROT AMY1 AEDAE Alpha amylase I precursor EC 3 2 1 1 1 4 alpha Launch analysis si P53354 D glucan glucanchydrolase 737 BlestP BE Launc
122. rence subentries that contain smith or jones It then combines these to create a list of those that contain both Smith and Jones in a single reference subentry It then takes the entries for each of the references matching the criteria This creates a single list of entries which contain references to papers which are co authored by Smith and Jones Searching for Subentries which Reference Papers that are Co authored by Smith amp Jones using the Standard Query Form If you wish to retrieve the subentry fields that are found rather than the parent entries the searches can be repeated with the retrieve entries of type set to Reference LION Bioscience 1 Repeat one of the above searches but set retrieve entries of type to Reference Reset search SWISSPROT Search Options Fields you can search Your search terms In a single field you can separate multiple values by amp m Search Combine search terms with amp AND bd e Reference Authors v smith Ref Auth li EE ZI Reference Authors jones AiTex E Get results of type AlTex Reference x Figure 3 13 Standard Query Form showing a query for subentries using the References Authors fields This search will retrieve the subentries that match the criteria rather than the parent entries Otherwise the search behaves similarly to the above so that searching for the two terms ina single text box combined with amp will produce reference su
123. rmat 3 The available viewing options are shown across the top of the page Text Entry SwissEntry 4 The option currently being displayed will be shown with the alternative entry shown as a hyperlink Click on the Text Entry hyperlink to view the entry using a text only format see Figure 5 8 119 120 Views Reset Entry Information AC Entry from Quick Select Searches Help Center o Databanks Results Projects Information Text Entry SwissEntry Previous Entry Entry 6 of 33 from Query 1 Next Entry 7 ox Entry Options RN Launch analysis tool RC Blast v Launch 2d Link to related information Link RT Save entry Save RN View Printer Friendly AI1M YEAST STANDARD PRT 834 AA PO3875 21 JUL 1986 Rel 01 Created 21 JUL 1986 Rel 01 Last sequence update O1 NOV 1997 Rel 35 Last annotation update COX1 OXI3 intron 1 protein AI1 Saccharomyces cerevisiae Baker s yeast Mitochondrion Eukaryota Fungi Ascomycota Saccharomycotina Saccharomycetes Saccharomycetales Saccharomycetaceae Saccharomyces NCBI TaxID 4932 1 SEQUENCE FROM N 4 STRAIN D273 10B MEDLINE 81069885 PubMed 6254986 Bonitz S G Coruzzi G Thalenfeld B E Tzagoloff Macino G Assembly of the mitochondrial membrane system Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase J Biol Chem 255 11927
124. rom the View results using drop down list see Figure 5 11 LION Bioscience Z Launch Microsoft Internet Explorer File Edit View Favorites Tools Help A Md gt QO x gl n DX e 6 Back Stop Refresh Home Search Favorites Media 4 i F History Mail Print Address a http kee 7313 srs71bin cgi bin wgetz Discuss e LION Help Center Quick Select Query 5 Custom i Searches Databanks Form Tools Results Projects Views Information BlastX More Info Result Display Options Job name Database to search temp SWISSPROT Updates imb Launch View results using lt amp Parameter set options Strand of query sequence to use Both V Codon Translation table Save current parameter set Standard Genetic Code M Blast View EMBL AA901739 Names only Comdletsrantas begin 1 1 ii 21 31 41 51 ttgtggatttccatagetgagggeccaggtctegegtttgggttgtgcaaagecccagge Bl n T 61 71 81 91 101 111 Sh a It end cgatcccagtcccccttcttgtcggacttgttaaccttcatccagtcatattcgecagtec iy raag 2 473 121 131 141 151 161 171 ue Mev tcaacgccaccggcatccttgagcgcctgagagaaaagttcgcggaggtagtcgtaatceg v Figure 5 11 Choosing a view to display results from one of the analysis tools 4 Launch the tool as usual see section 1 7 Using Analysis Tools p 20 The results of the analysis will be displayed on the Query Result page using the selected view 5 3 Creating Views So
125. s that match dehydrogenase 4 Click the search j button This runs the query and then displays the Query Result page showing your results 6 SRS Quick Tour SRS Reset Query SWISSPROT alltext dehydrogenase found 3987 entries next SWISSPROT 12AH CLOS4 p21215 12 alpha hydroxysteroid dehydrogenase EC 1 1 1 176 29 C selected results only Fragment unselected results only SWISSPROT 25KD SARPE P23170 Development specific 25 kDa protein 258 SWISSPROT 2BHD STREX P19992 20 beta hydroxysteroid dehydrogenase EC 1 1 1 53 255 Result Options SWISSPROT 3BH1 MESAU 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type I 3Beta HSD I Includes 3 beta i 7 hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 Deunchranalysts tool Q60555 3 beta hydroxy 5 ene steroid dehydrogenase 372 BlastP Launch Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase Show tools relevant to these I SwISSPROT 3BHi MOUSE 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 results Tools isomerase type I 3Beta HSD I Includes 3 beta p24815 hydroxy delta S steroid dehydrogenase EC 1 1 1 145 372 Link to related information 3 beta hydroxy S ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC Link 5 3 3 1 Delta 5 3 ketosteroid isomerase Save results Save SWISSPROT 3BH1 RAT 3 beta hydroxysteroid dehydrogenase de
126. s A and B using the operators lt and gt A gt B gt B3 A B B4 A5 A6 List all the entries in set B List all the entries in set A that have links with set A that have links with set B Figure 8 3 Linked Data Links are not usually bidirectional however the link indices in SRS are used bidirectionally For instance A gt B This retrieves those entries in B that are linked to entries in A A lt B This retrieves those entries in A that are linked to entries in B LION Bioscience 171 8 3 5 Use of Operators to Combine Search Items Combining queries allows you to refine your search results This can be done using logical operators OR AND BUTNOT see section Logical Operators p 169 or link operators see section Link Operators p 169 Note that link operators take precedence over logical operators Example 8 2 Simple linking This example searches for links to a specified databank in the results of an index search swissprot des kinase pdb The result will be a list of all the entries in the PDB databank that have links to the results of the index search swissprot des kinase See section 8 2 Searching in Indices p 157 for an explanation of index searches Example 8 3 Multiple linking 1 It is possible to combine several linking queries For example swissprot id acha human prosite swissprot The search first retrieves the SWISS PROT entry acha human T
127. s hea kee wes 173 Links with Sets Containing Subentries 174 8 5 Storing Intermediate Results in Sets 0005 176 INDEX 4 SuwExso 333 REX NAESCURTEE SUE ORR ANE Ee ORE Ke UE E dE x ess Ce ees 145 CHAPTER SRS QUICK TOUR SRS is the world s premier data integration analysis and display tool for bioinformatic genomic and related data This chapter contains a guided tour of SRS which will help you become familiar with the SRS web interface During the guided tour you will learn How to start an SRS project How to perform a query using SRS How to link your query results to other databanks How to change the way in which your results are dis played by creating your own view How to run an application How to save your working project SRS Quick Tour 1 1 Introduction This chapter is intended to introduce new users to SRS It will take you through some basic procedures that you can expect to do with SRS It is intended as an introduction and will get you started but it is not intended as a complete description of the software If you want more detail of how to do a certain task refer to the relevant chapter of this guide The notes in the margins tell you which chapter is relevant to each set of steps If you want to know more about a particular SRS page then you should refer to the relevant page in the SRS Online Help You can get to the Online Help by clicking on your SRS page
128. s section will take you through running a tool on a set of results 1 Go to a Query Result page If you can t remember how to get to the Query Result page use the Results tab to go to the Manage your Query Results page tick the check box beside a set of LION Bioscience results set the view to something appropriate e g default view and click the Rerun Query button to take you to the Query Result page for that set of results Select an entry from the list of the results by ticking the check box beside it It will be the information in this entry that is then used to run the tool Click the Teels button This will take you to the Tool Select page which shows all the applications that can be used on the current entry You may need to open up the lists of tools by clicking on the next to a group 21 22 SRS Quick Tour Pd LION Help Center O Custom Views Information Quick Select Query Searches Databanks Form Tools Route Projects SRS Query SWISSPROT ID 12AH CLOS4 found 1 entries Quick Launch Available Analysis Tools listed by type Expand all Collapse all Launch analysis tool antigenic Alignment Tools Display Tools Launch Edit Tools l Information Tools Nucleic Tools EE Protein Tools Similarity Search Tools BlastP BLASTP Protein Protein Sequence Similarity Search Launch More Info TBlastN Sequence Similarity Search Launch Mo
129. se EMBL MAORF SWISSPROT 3BH1 MOUSE SWISSPROT 3BH1 RAT 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type I 3Beta HSD I Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type I 3Beta HSD I Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase EMBL MMHSD3B EMBL RN3BHSDA SWISSPROT 3BH2 MESAU 3 beta hydroxysteroid dehydrogenase delta 5 gt 4 isomerase type II 3Beta HSD II Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase EMBL MAHSD3B SWISSPROT 3BH2 MOUSE 3 beta hydroxysteroid dehydrogenase delta 5 4 isomerase type II 3Beta HSD II Includes 3 beta hydroxy delta 5 steroid dehydrogenase EC 1 1 1 145 3 beta hydroxy 5 ene steroid dehydrogenase Progesterone reductase Steroid delta isomerase EC 5 3 3 1 Delta 5 3 ketosteroid isomerase Fragment EMBL MM3BHYDRX SWISSPROT 3BH2
130. set C selected results only unselected results only Result Options Launch analysis tool Bas launch Show tools relevant to these Tools results Link to related information Link Save Save results Display Options View results using SeqSimpleView z Sort results by unsorted z ascending C descending Show 30 x results per page Printer friendly view Apply Display Options next Apply Options to SWISSPROT lAccession ____Description __ Seqlength SWISSPROT 143F MOUSE 14 3 3 protein eta Protein kinase C inhibitor P 11576 protein 1 KCIP 1 245 SWISSPROT 143G BOVIN 14 3 3 protein gamma Protein kinase C inhibitor P29359 brotein 1 KCIP 1 2m SWISSPBROT 1437 MOUSE 14 3 3 protein zeta delta Protein kinase C inhibitor P35215 protein 1 KCIP 1 Mitochondrial import 245 stimulation factor S1 subunit r Lm are I SWISSPROT 143Z SHEEP 14 3 3 protein zeta delta Protein kinase C inhibitor P29361 protein 1 KCIP 1 oe FETE Fes l SWISSPROT AAIP WHEAT Abcisic acid inducible protein kinase EC 2 7 1 202066 Fragment 332 I SWISSPROT AAK1 PIG 5 AMP activated protein kinase catalytic alpha 1 Q09136 chain EC 2 7 1 AMPK alpha 1 chain 63 kDa 132 subunit AMPK Fragments ID SWISSPROT AAK2 PIG 5 AMP activated protein kinase catalytic alpha 2 Q29948 chain EC 2 7 1 AMPK alpha 2 chain Fragment 129 I SWISSPROT AAKB PIG
131. ste Hp A Mar 2002 1 m uen m vvvv I Lastupdated cot MT H H D A o Sequence Length gt es v Figure 3 7 Extended Query Form querying EMBL for entries about histamine in humans that were added to the databank after 1st March 2002 The search uses the Description Organism and Entry Creation Date fields 67 Querying with SRS 3 4 Subentries 3 4 1 About Subentries Subentries are parts of data entries that have an internal structure which needs to be conserved when searching a database A typical example of this might be a databank whose entries contain multiple literature references or one that contains features e g within a sequence in which the relationship between the features is important 3 4 2 Use of Subentries Subentries are particularly useful for queries where a relationship between items is important Suppose a user wants to search for references written jointly by authors Smith and Jones but does not want to find papers written by only one of those authors In a case like this it becomes important that the user can search for data where Smith and Jones occur within the same literature reference whilst excluding entries that only contain papers written by each author separately with no papers authored jointly by Smith amp Jones A search of entries even where it is specified that both Smith and Jones must appear within an entry will reveal all entries containing references by Smit
132. sult page Help Center O Quick Select Searches Databanks Projects i Information SRS Reset Query embl Description kinase found 73271 entries next EMBL 400229 400229 Artificial sequence for kinased linker R140 O selected results only EMBL 401166 401166 Artificial sequence derived from yeast phosphoglycerate 1207 9 unselected results only kinase PGK gene EMBL 401168 401168 Artificial sequence for kinased linker R140 24 Result Options EMBL 415367 415367 phosphoglycerate kinase gene 425 Launch analysis tool EMBL 416530 416530 Synthetic pyruvate kinase gene SEQ ID NO 1 3602 BlastN v Launch EMBL 416753 416753 tie receptor tyrosine kinase seq ID No 3 3845 EMBL 416754 tie receptor tyrosine kinase alternatively spliced to lack one Show tools relevant to these A16754 of the epidermal growth factor homology domains seq ID No 3713 results Tools 4 Link to related information EMBL 421640 421640 protein kinase gene 1403 Link EMBL 422127 422127 partial protein kinase protein of ILTV 656 Save results Save EMBL 422428 422428 Kinased linker P140 24 EMBL 426374 426374 M musculus HSY thymidine kinase 5 non coding region 60 Display Options EMBL A27171 A27171 Tyrosine kinase receptor gene 2966 2 3 EMBL 429799 429799 S cerevisiae pyruvate kinase gene 5 terminus 49 View results using SegSimpleView wl E
133. t p si ID p M r Accession Number el n Primary Accession Number rH Description n O pz m S M m Entry Creation Date select fi Jan vvv hn sj Jan gt wy n LastSequenceUpdate selet i 2 van fry ft an I rw E LastAnnotationUpdate select gt fi Jan z hy hx Jan gt vvv m Figure 3 28 Extended Query Form showing hyperlinks for datafields From the List Of Databanks Page The Information tab takes you to the List of Databanks page Here you will see a list of the available databanks Clicking on the hyperlink for a databank will take you to its 89 Querying with SRS Databank Information page This contains a section listing the datafields for the relevant databank PEICRIIJCESIEELSE Field Name Short Name Type No of Keys No of Entry References Indexing Date Status AllText all group 0 not indexed ID id id 101602 101602 25 Feb 2003 ok Accession Number acc index 119193 119300 25 Feb 2003 ok Primary Accession Number pac index 101602 101602 25 Feb 2003 ok Description des index 58091 578507 25 Feb 2003 ok Gene Name gen index 83823 145372 25 Feb 2003 ok Keywords key index 840 370433 25 Feb 2003 ok Entry Creation Date crd date 40 101602 25 Feb 2003 ok LastSequenceUpdate Isu date 40 101602 25 Feb 2003 ok LastAnnotationUpdate lau date 39 101602 25 Feb 2003 ok Organism Name org index 10800 236202 25 Feb 2003 ok Taxon tax inde
134. t are Co authored by Smith amp Jones using the Standard Query Form In the above example entries were retrieved that referenced papers by Smith and Jones but without concern for whether Smith amp Jones were co authors of any papers If you wish to search for entries that reference papers that are always co authored by Smith amp Jones you should modify your search so that rather than searching in two separate text LION Bioscience boxes on the Standard Query Form you search for both authors in a single text box 1 From the Select Databanks To Search page select a databank to search e g SWISS PROT and go to the Standard Query Form 2 Use the first drop down datafield list to select an appropri ate subentry field e g Reference Authors 3 Inthe text box beside the datafield you have used type smith amp jones Note Make sure you use the amp sign which tells SRS that you want to look for both authors combined using the boolean operator amp AND rather than OR or NOT Reset search SWISSPROT Search Options Fields you can search Your search terms In a single field you can separate multiple values by amp m Search Combine search terms with amp AND ae e Reference Authors v smith amp jones i AllText ka Use wildcards M e AiTex M Get results of type AiTex z Entry Figure 3 11 Standard Query Form showing a query for entries using the References Authors su
135. t hand text box You do not have to use all four rows but greater detail may help refine your search Use Combine search terms with drop down list to spec ify the method by which the various search terms should be combined amp AND OR or BUTNOT Choose the type of entries you wish to retrieve using the Get results of type drop down list Leave it set at Entry for this example Choose a view using the View results using drop down list or choose Create a view See chapter 5 Views p 109 for more information on views Specify the number of entries to display per page using the drop down list Click the Search button LION Bioscience SRS Reset search EMBL Search Options Fields you can search Your search terms In a single field you can separate multiple values by amp Im Search Combine search terms 1 j with amp AND X e Keywords kinase i Entry Creation Dat 01 Jan TERRENT Entry Creation Date 01 Jan 2002 AllText Get results of type AlTex Entry Result Display Options Create a view Select the fields you want displayed in your view and choose the format View results using SeqSimpleView Choose 1 or more fields Display As Table List or Sequence Format amp mpl C Create a view Primary Accession Number Show 30 zl SeqVersion Molecule Description xl TEY To do more advanced queries use the
136. tabanks for which the view will be available using the left hand column of databanks headed Data banks to define a view for These are the root databanks for the view 6 Select the databanks to which you wish to link using the right hand column of databanks headed Databanks to be linked to 131 132 Views Databanks to define a view for Databanks to be linked to Show fields from C All fields in EMBL EMBL reference EMBL features EMBL counter 5 PROT SWISSPROT_reference SWISSPROT comment SWISSPROT feature SWISSPROT counter EMBL Release EMBLRELEASE_features EMBLRELEASE_reference EMBLRELEASE_counter EMBL Updates databanks Common fields only EMBL_reference EMBL_features EMBL_counter SWISSPROT SWISSPROT reference SWISSPROT comment SWISSPROT feature SWISSPROT counter EMBL Release EMBLRELEASE features EMBLRELEASE reference EMBLRELEASE counter EMBL Updates zl m Create New View Figure 5 20 Selected databanks 7 Click on the create New View button see Figure 5 21 Reset Create View Options Databanks to define a view for Databanks to be linked to Show fields from All fields in databanks Common fields only View name EMBL myTestview EMBL reference EMBL features Display results as EMBL counter table ROT SWISSPROT reference C list SWISSPROT comment SWISSPROT feature SWISSPROT counter EMBL Release EMBLRELEAS
137. tracellular sporulation specific P08019 EC 3 2 1 3 Glucan 1 4 alpha glucosidase 549 1 4 alpha D glucan glucohydrolase I SWISSPROT AMYH YEAST Glucoamylase 1 S2 precursor EC 3 2 1 3 P08640 Glucan 1 4 alpha glucosidase 1 4 alpha D 1367 glucan glucohydrolase SWISSPROT ARi16 YEAST P40518 ARP2 3 complex 16 kDa subunit P16 ARC 154 I SWISSPROT AXL2 YEAST P38928 AXL2 protein precursor SRO4 protein 823 SWISSPROT BNR1 YEAST P40450 BNI1 related protein 1 1375 r Coatomer epsilon subunit Epsilon coat 296 Figure 3 18 Quick Search of SWISS PROT for smith amp jones 3 5 Expression Queries 3 5 1 Searches using a Query Expression You can make queries using a query expression Figure 3 19 which you will find on the Manage your Query Results page You can also use this method to combine link or refine the results of existing queries Search using a query expression Im Search J Figure 3 19 Expression text box Querying with SRS 3 5 2 Using Expression Queries 1 On the Manage your Query Results page enter your query into the Search using a query expression text box 2 Click on the Search button For example to search for all entries that satisfy two existing queries Q1 and Q2 you could type Q1 amp Q2 gt i z This will return a new listing Q3 that has all entries that are in both Q1 and Q2 If you wanted to search for the entries in query Q3 that had links to the
138. try page shown using Text Entry format 103 104 Links to Additional Data Click the tink button This will display the Link page for single entry linking see section 4 3 Index Links p 95 4 5 Expression Linking The Query Expression text box e g on the Manage your Query Results page is a useful alternative to the linking methods discussed earlier in this chapter It can be used to search for a link between two or more sets of results or between a set of results and a databank Note Using the Query Expression text box allows you to search for links without going through the Link page 4 5 1 Expression Linking Procedure You might be interested in the entries from a set of DNA sequences in Q1 that are linked to a set of protein sequences in Q2 If there are links between entries in the queries you have the choice of returning the entries in Q1 that have links with Q2 which is what is wanted here or of returning the entries in Q2 that have links with Q1 See also the section 4 5 2 Linking Operators p 105 The Query Expression text box is shown in Figure 4 11 You should enter your expression e g Q1 lt Q2 as shown LION Bioscience 105 LION Quick Select Query Searches Databanks Form Toots SRS Help Center 7 Results Projects guion Information Reset Results Options Search using a query expression 5 05 Im Search Figure 4 11 Expression linking T
139. ue this is indicated on the Launch page prior to launching Figure 6 4 P LION Help Center 2 Quick Select Query Searches Databanks Form Tools Results Projects REE Information SRS V Reset BlastN More Info Job Options Job name Database to search TENER temp EMBL Updates v m Launch Note this tool is run by LSF batch queueing system Select a queue to submit jobs EMBL AA901762 begin to blast m sisley batch an 1 1i 21 31 41 51 tgtataaccaccctcacaaacgatggcatggtacgeccgcaacctagcaaaggcccacaa 61 T1 81 91 101 111 Parameter set options end gggteccattgtcacceggctaagageatcttccecgeggeatccacgagacgecggagg 580 121 131 141 151 161 171 al Save current parameter set ih hl Kd ak Led t ates ich Kl as Strand of query sequence to use Both Figure 6 4 Typical SRS batch queuing message from a Launch page for a run of BLASTN 6 4 3 2 Tool Invocation Page for Batched Tools After the Launch button is clicked the Tool Invocation page will be shown 4t LION Y Help Center 2 Quick Select Query Custom Searches Databanks Form Toots Results Projects Views SRS Information Tool was submitted to Queue blast m sisley batch Tool command blastall p blastn d srsdata flatfiles blast emblnew i temp blastn 1 in lt gt Use Batch job status page to view the results Figure 6 5 Tool Invocation page for batch processing 143 144 Analysis Tools 6 4 3 3 Accessing the Results The
140. ulase 3 2 Quick Searches 3 2 1 SRS Quick Search Page Depending on the databanks which are available in your SRS installation you may be able to perform a small number of Quick Searches from the SRS Quick Search page Typically you will have the following searches available Quick Text Search Sequence Similarity Homology Search These allow you to make some pre formatted searches without needing to understand SRS in great detail For more information see the help files for the SRS Quick Search page Querying SRS Quick Search in the Online Help pages 3 2 2 About Quick Search Quick Search works by searching all datafields of type text in the selected databanks and is an alternative method of generating query results fast without using the query forms LION Bioscience If you do not get the results you expect then a slight change to the search phrase may help to target your search and thus may yield improved results Alternatively try one of the other search methods as these allow you to specify your area of interest in more detail Help Center O SURE Databanks ed Results Projects stam Information SRS Reset Quick Search LU d CEP Figure 3 2 The location of Quick Search on the Select Databanks To Search page Note The Quick Search option combines all the fields with a data type of Text using the OR operator 3 2 3 Using Quick Search Quick Search allows you to search with a minimum number o
141. unter EMBL Release EMBLRELEASE_features EMBLRELEASE reference EMBLRELEASE counter EMBL Updates xl I Create New View Delete View Figure 1 11 Create your own views Steps 2 7 Click the create New view button to display the View Man ager page 2 from which you can select the fields for your views see Figure 1 12 8 Choose the fields you want to view by ticking the check boxes beside them For the purpose of this example select the Description field for both databanks Note The field names are also hyperlinks to the Field Infor mation page see also section Information Pages Field Information in the Online Help which contains information about each field 15 16 SRS Quick Tour Create View Options Select the datafields you want displayed in your view using the checkboxes View name myTestView Save view Save Datafields for your primary databanks SWISSPROT F ID AccNumber Prim ccNumber lv Description GeneName Keywords DateCreated P LastSequenceUpdate LastAnnotationUpdate Organism Taxon NCBI TaxId Organelle ProteinID I checksum DbName DBxsref SegLength Sequence fasta hd Fields of subentry Reference Authors L Title Journal volumeNo FirstPage Year MedlineID PubMedID RefPosition RefcommentCode M RefComment Fields of subentry Comment CommentType Comment Fields of subentry Featu
142. utton on your browser to return to the Standard Query Form 6 Click one of the Search buttons This runs the query and then displays the Query Result page showing your results Results are listed by default in the order in which they are stored in the databank unsorted To make it easier for you to find the results you want you can use sorting to reorganize them Sorting is particularly useful if you have a large number of results 1 To sort a set of results choose the required sort order from the Sort results by drop down list in the Display Options box e g Organism Name Sequence Length 2 Use the option buttons to choose whether to sort in ascending or descending order LION Bioscience Display Options View results using SeqsimpleView h Sort results by Organism Name E C ascending descending Show 30 v results per page Printer friendly view T Apply Display Options Figure 1 7 Sort by Organism Name in an descending order 3 Press the Apply Display Options button to sort the results 1 5 Links See Links to Additional One of the many features of SRS is its ability to search for ae Chapter 4 for more links between your current results and related information in information other databanks In this example you will search for links from one of your SWISS PROT results to related entries in EMBL 1 5 1 Linking to Related Information 1 On the Query Results page tick the check box n
143. ve Rename project Trensit Peptic Renam f Delete project Delete J Copy selected items to project Copy Figure 2 11 Personalized project names CHAPTER QUERYING WITH SRS One of the greatest advantages of using SRS is its ability to search databanks and the range of methods available to do so This chapter introduces you to the ways in which you can perform a query using SRS By the end of this chapter you will have learned e What a search term is and how to construct one How to perform a Quick Search How to use the Standard Query Form and Extended Query Form What subentries are and the advantages of using them in queries How to search for entries that relate to a specific expression or phrase Expression Query How to sort your query results How to browse the index Querying with SRS 3 1 Search Terms Whichever search method you use you will need to use some sort of search term Search terms used in SRS can be categorized as follows Single word search see section 3 1 1 Single Word Searches p 56 Multiple word phrases see section 3 1 2 Multiple Word Searches p 57 e Numbers and dates see section 3 1 3 Numbers and Dates p 57 Regular expressions see section 3 1 4 Regular Expres sions p 59 Wildcards see section 3 1 5 Wildcards p 59 The rest of this section explains how search terms are constructed The individual s
144. view T Apply Display Options Figure 5 1 Typical drop down list of available views 5 2 1 How to Apply Views This section gives instructions for applying views to your query results In the first example you will begin by querying a databank and setting the query options for views so that the query results are displayed with your chosen view The other 111 112 Views examples show how to apply your view to an already existing set of results Applying a View From the Standard Query or Extended Query Forms Whenever you query a databank using either of the query forms you can also choose from a drop down list a view to be used to display the query results This example shows you how to apply a view from the Standard Query Form On the Extended Query Form the contents of the Result Display Options box are slightly different but the basic steps are similar To apply a view to a SWISSPROT query from the Standard Query Form 1 On the Select Databanks To Search page select the SWISSPROT databank using the check box beside it and click the Standard Query Forn button See chapter 3 Querying with SRS p 55 for more information 2 Enter oxidase in the text box The default AllText datafield is fine 3 Inthe Result Display Options box select a view from the View results using drop down list See Figure 5 2 LION Bioscience Result Display Options View results using SegSimpleView Names
145. w permanent projects within an account and move between them see also section 2 4 2 Switching to Another Project p 48 Note This feature is not available for temporary projects To create a new project 1 Click the New Project button This will start a new project and display the Select Databanks To Search page 2 4 2 Switching to Another Project The Project Manager page allows you to move between projects that have been saved in your account Note This feature is not available for temporary projects To return to a project that you have already saved LION Bioscience 1 From the Project Manager page select the project you want to resume from the drop down list in the Other Projects box 2 Click the S itch button The project you have just selected is now displayed on the Project Manager page You can work with this project as usual 2 4 3 Copying Project Information You can copy information such as views and queries from one project to another Note This option will only be available if you have more than one project in your account This option is not available for temporary projects To copy project information 1 Make sure you are in the project from which you want to copy items see section 2 4 2 Switching to Another Project p 48 Select the items you wish to copy by tick ing the check boxes beside those items Contents of project Views Name Query Expression Name Iv Q
146. w from the Extended Query Form LION Bioscience 129 1 Enter your search term s as usual See chapter 3 Querying with SRS p 55 for details 2 Use the drop down list to choose whether the view will dis play as a table or list view 3 Tick the check box to the right of any fields that you want to display in the results 4 Continue with your query as usual Typical results for table and list views are shown in Figures 5 15 and 5 16 respectively 5 3 2 Creating Views using the View Manager Pages If the built in views do not do what you need and the options on the Query Forms are insufficient you can use the View Manager pages to create views Note There are two View Manager pages referred to here as View Manager page 1 and View Manager page 2 Click the Views tab to go to the View Manager pages You can control the following elements of any views that you create The name of the view View Manager page 1 Whether the view displays as a table or list format View Manager page 1 Whether the fields show on View Manager page 2 will include all available fields or just the common ones View Manager page 1 130 Views The list of databanks for which the view is defined and for which the view is therefore available These are referred to as root databanks View Manager page 1 The list of databanks that may have a link with the entries View Manager page 1 The list of fields from
147. which the expression is performed e g the name of a databank or a set etc Table 8 4 Typical SRS operands Operand Example Meaning Databank EMBL Each databank has a unique name name Setname Ql SRS gives each query a name which can be used when you want to perform an operation on the set of results from that query Index embl This command initiates a search in search des one or more indices of one or kinase more databanks Expres Q1 amp Q2 Ifan expression is enclosed in sion parentheses it is treated as a sin gle operand Parentheses can be nested to any degree Parent parent This is a special operand that allows the conversion of a set of subentries into a set of entries see section 8 4 Entries and Suben tries p 173 167 168 SRS Query Language 8 3 4 Operators Operators tell SRS what to do with the operands e g search for links between two operands Table 8 5 shows a list of available operators For more information on the types of operator see section Logical Operators p 169 and section Link Operators p 169 For information on the use of operators see section 8 3 5 Use of Operators to Combine Search Items p 171 Table 8 5 SRS query language operators Operato r Type Meaning Logical OR amp Logical AND Logical BUTNOT This operator may need to be escaped in UNIX using gt Link Link keeping items in the set to the right
148. x 4834 940067 25 Feb 2003 ok NCBI TaxId txi num 7101 104471 25 Feb 2003 ok Organelle ogn index 559 11670 25 Feb 2003 ok ProteinID prd index 160681 163655 25 Feb 2003 ok Checksum cks index 101503 101602 25 Feb 2003 ok Figure 3 29 Part of the Databank Information page for the SWISSPROTRELEASE databank showing datafield hyperlinks Click on one of the datafield hyperlinks e g Description to go to its Field Information page see Figure 3 25 Note SWISSPROT is a virtual databank This means it is made up from other databanks e g SWISSPROT Release and SWISSPROT Updates If you look at the Databank Information page for SWISSPROT you will not see all the information that is shown in Figure 3 29 if you want all the detail you need to look at the individual component data banks CHAPTER LINKS TO ADDITIONAL DATA After you have queried a databank using SRS you may find that you want to refine your search further For example you may want to find further information on the entries returned by your initial search e g by looking for related entries in another databank Alternatively you may have queried a databank that returned several entries relating to your query but you only want to know about the entries that relate to a specific protein During this chapter you will learn How to use SRS links to find entries which are related to each other in more than one databank Links to Additional Data 4 1 What is a Link
149. y entries that have links to the SWISSNEW databank Using this technique it is possible to retrieve the entries for kinase but exclude any that are replaced by more up to date entries in SWISSNEW LION Bioscience 173 The distinction being made here is that entries in SWISSNEW will not be linked to themselves or other entries in SWISSNEW so all the SWISSNEW entries will be kept However any entry in SWISS PROT that has been replaced by an entry to which that entry is linked in SWISSNEW will be picked up and rejected In this way out of date entries are excluded Note The first part of the query also defines a group a which contains the SWISS PROT and SWISSNEW databanks This is used in the second part of the query rather than listing the databanks explicitly see section 8 2 6 Searching Multiple Databanks p 164 Example 8 6 Searching multiple databanks and screening for over laps Many protein or DNA databanks overlap to a great extent which creates a lot of redundancy however the annotation of equivalent entries in different databanks can be quite varied This can be useful for string searching because the probability of finding a certain enzyme name is greater if you can search all sequence databanks After the search links can be used to remove any overlaps See Example 8 5 Complex linking for how this might be done 8 4 Entries and Subentries Sets originating from the same databank may have different

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