COMMUNITY ANNOTATIONS USER MANUAL Table of
Contents
1. Figure 8 This will direct you to a page showing the detailed information about the term you selected e g parent term and child term relationships or more general terms vs specific terms Figure 9 Click Select this term if you are satisfied with it Figure 9A you will be redirected to a page similar to Figure 6 see above with the GO term filled in Next insert the publication that provides the evidence for the GO term There are two ways to insert your citation 1 Insert the PubMed ID PMID which can be found on either the summary or the abstract page of the article in PubMed You can use the Open Entrez PubMed link to search for the article Figure 6B this will open a new page 2 You can manually type or copy and paste in the citation if it 1s not in PubMed Figure 6C e g meeting abstract or dissertation If the article is in PubMed please use the PMID because PubMed and the annotation databases can then be linked by this identifier After you have inserted the citation select the Evidence Code from the drop down menu indicating the type of data that supports the GO term To familiarize yourself with the evidence codes click on the link Guide to Gene Ontology Evidence Codes Figure 6D When you are finished Figure 6 MGOS Figure 6 ome gt AGCoL Gene Details gt Annotation for MMGa05621 gt Gene Ontology Term for MMGa05621 Gene Ontology Term for MMGa05621 Usage note If you use the PubMed Id field the citati2. CD H Publications Donofrio NM Oh Y Lundy R Pan MM Drown OU Jeong JS Coughlan 5 Mitchell TK Dean RA Glebe Gene e2oresesion during NRTG starvation in the rice Digest fungus Meureporthe arises G Fungal Genet Diol 2006 Sen 4369 G605 17 Pf viderm e manage a Gene replacement Moni F Gene repiacement Local Diant with Codina Saauenos Locali Diast with Protein Seavence MCE Diast with Codina Secuenrce MOE Dist with Protein Seavence AVE TCE AT CVC ACEC CEM AASLIATATTCAAGOTOTTC AAC CAGGALTTTATC OT OGCALEAACLCOTTACACTIOTCACCAAGGA ACT Cotes T TCAGOGOGGAGOGCEOTACOGTATCOTGOTOCOCCOCCOTTAATAACCAGACOTCECCGOGACOOGTOT TCA TCAACIAACIOITICACTCA ATESTTTITCACRICAAGAAAAT OC TAGE CAA CO OCCT TOC OC AGATC AAS TT CT OCACSCAT TT Ce GAG CACCETAACATTA CATOAITCTCTAT ACA FOGACATACCOCOCCCAGATAAC TICAACGCAGACCTATCTCTA FOAACAOCCTOATOMAAGCTUOTOATC TOG CTSCCATTIT ATC CATCAC OCCA CCCOT TAC COA TOC ACTTICOOCASSTOST TT CATCTACCAGAT ICTS Tee Oecrc eT AACITACAT ACACT CACC CAATOT OCT GCACCOTGATT ET GAAACC CO AAAC TIC TCOTCAACOCOGATIOC GAC TOAAGATTIIOCGAcCTT TESST CST Tee COC ee Tee TT eT Cece TOCA CTC ALAA CLAAC OIC TEI TI ACATOAC TOAATA TCS CCC Tr ACCACHI TOs TAcccu nre Trenmecrtet Seqwerce CALCTRASL ATT ATES TEAC TICE AAACC TAT AL GAAAEC GATT GATEOTA TESTE GOTIOGATOCATTT IG AGA TOC TSS BACOICAOIOICCCT ICT CAAT COCrCOAT TACO COACCACIC TCAACCACGAAT CCT ICATAT ACT Ceti ACACCUAAC UALCHMAAC ACOCTIT CSE GAATISOSTNT COCO CACC CAGCGAGTALC OTC COGAAC CTC CEST TCA TOO C
3. Select the appropriate Evidence Code from the drop down menu When you are finished adding the information click Save and your data will be appended to the identifier The Fungal Figure 9 MGOS Sitemap Figure 9 home gt Gene Ontology Term for MMGa05621 Gene Ontolo Term for MMGa05621 acetylcholinesterase activity lt Search Browse page acetylcholinesterase activity elect his erm A More General carboxylesterase activity More Specific all gt molecular function gt catalytic activity gt hydrolase activity gt hydrolase activity acting on ester bonds gt carboxylic ester ee Catalysis of the reaction acetylcholine H20 choline acetate hydrolase activity gt carboxylesterase activity Anatomy Ontology is also a work in progress If there are terms that should be defined but are not listed please contact Anupreet Kour akjosan email arizona edu or Kevin Greer kevin agcol arizona edu they will assist with updating the ontology If you have made a mistake and need to start over click on the Cancel button None of your Fungal Anatomy information will be saved in the database H Publications 1 Figure 4G Add a citation Click on Add a citation Figure 4G to get to the citation page Either insert the Pub Med ID or manually type or copy and paste in the reference information If you inserted a Pub Med ID press the enter or return key on your keyboard and the citation information will be populated
4. automatically Click on the Save button to add the reference to your annotation or Save and New if you plan to enter additional references 11 Figure 4H Edit a citation If you want to make changes to a paper that is listed as a citation for the gene click on the pencil near the citation as shown in Figure 4H and make changes in the page that opens D Mutants 1 Figure 47 Add a Mutant The Add a Mutant link Figure 4 will take you to the page where you can add the name Description and type of the mutant Images can be added for the mutant by clicking on Browse in front of Image file field Following options are available on mutant assay page Figure 10 Edit Mutant M3HS1 Figure 10 K Figure 104 One can add strain name eg 70 15 Guy11 etc in this column on which assays had been done Figure 108 Name of the mutant is required for second column Figure 10C Third column is for mutant description 1 e how these mutants are generated or what is the resistance cascade introduced in the wild type strain like hygR Figure 10D Fourth column is for the description of the mutant whether these are insertion deletion mutants Figure 10 Under this column one can add some images related to a particular assay Figure 10F The above entered information can be saved by clicking on save button Back button directs the link to move to Gene annotation page Moreover save and new button can be used
5. basic description of the history and researchers involved in generating the database 2 Forum This page allows one to register as a community annotator The steps are as follows a Click on forum b You will see several options as shown in Figure 1 c Click on register Figure 1A d This will take you to the page where you can enter your e mail address for MGOS e After registering you can use that e mail address to get into the forum and you can use several available features there These are 1 Join or start a discussion thread on a topic of community interest 11 Leave comments or suggestions for using MGOS features you would like to see added comments on existing data etc 3 4 IRBC Abstracts access to the abstracts of the Foruth International Rice Blast Conference Changsha China October 9 14 2007 Figure 1 MGOS Magnaporthe grisea Oryza sativa Interaction Database Forum July 27 2008 11 28 45 AM Welcome Guest Please login or register Fi gure 1 Forever Login Login with username password and session length News The Magnaporthe grisea Oryza sativa Interaction Database forum is now live Search _y HELP SEARCH CALENDAR LOGIN REGISTER _ I MGOS Magnaporthe grisea Oryza sativa Interaction Database Forum Board name Topics Posts Last post Getting Started February 13 2007 04 58 20 PM boa 2 2 in Welcome to the MGOS Foru A brief description of how to get start
6. editing click on the icon or link add information and click the Save icon diskette to the left of the box If you incorrectly opened a field click on the cancel icon Figure 3 MGOS Community Annotations Figure 3 Login Sitemap home gt Community Annotations Search for Gene to Annotate Magnaporthe oryzae Bist Sequence Paste your nucleotide or amino acid query sequence in field below susr B Instructions 1 To begin annotating a gene you may either search based on its name symbol or accession number using the basic gene search below or you may blast the sequence against the existing gene models by pasting your sequence into the text box in the blast section below and clicking the BLAST button 2 Depending on the results of your search you may be presented with a list genes at which point you simply need to click on the gene accession number which begins with MC_ that you are interested in to begin the annotation process In other cases you will be taken directly to the annotation screen 3 If your gene cannot be located using either on of these methods please contact us at mqos maosdb org so that we can provide further assistance 4 You may also perform a more elaborate serch for genes to annotate using the Advanced Gene Search page or provide additional parameters to the blast algorith using the Blast page 7 Sections of the Gene Page Gene page is further divided into several sections that can be ann
7. to save changes in the previous window and open the new window to add new mutant Figure 10G Assay name can be selected by scrolling down select assay option Figure 11 MGOS n Figure 11 home gt AGCoL Gene Details gt Annotation for MMGa05621 gt Gene Ontology Term for MMGa05621 gt Find Gene Ontolo Term for MMGa05621 gt Gene Ontology Term for MMGa05621 gt Add or Annotation a Mutant gt Transcript for MMGa05621 Transcript for MMGa05s5621 Transcript successfully loaded Transcript being edited Strand Chromosome Chromosome Relative Relative Start Stop tart Stop Length Delete 1771241 1771399 0 159 1771482 1772705 241 1224 1772769 1773194 1528 426 1773375 1773529 2134 155 1773606 1774332 2365 727 New Exon BLAT a Transcript Sequence P T Chromosome Relative CDS Start 1771241 0 CDS Stop 1774332 3091 Product Name lunjgrot ID QOPND9 MAGGR Multifunctional beta oxidation protein EC 4 2 1 EC 1 1 1 Validate Cancel Figure 10H Assay description like conditions media experiment description can be added in this window Figure 12 MGOS Sitemap Figure 12 home gt AGCoL Gene Details gt Annotation for MMGa05621 gt Gene Ontology Term for MMGa05621 gt Find Gene Ontolo Term for MMGa05621 gt Gene Ontology Term for MMGa05621 gt Add or Annotation a Mutant gt Transcript for MMGa05621 gt Blat Search Page BLAT SEARCH Database riceblast fasta Quer
8. 9 02 09 14 17 59 014352 Chromosome Linkage Groupo Gene Symbol Synonyms Gene Description Gene Comments Location Secreted Protein 4064005 40095974 21 408389127 40655 4008 381 27 408 132090274 40646071 40642704 4064 206 40044 77 4064491 4064805 Trenecriots Act a Trenecrigot Aira ores Tronnoripit models HEO Oomer i togt ative ed praler amp rase spel lt i24m rvt gt o CE gt t gt trnmedt we te erence ket models HOG VIDTE i heer snt iwetiendt geretecirs h irnrs e spasil Ve eeremee ipi Hedel 681 8 gpeeeeeres ot r ECI PEFS is oS 1 CCE Overte ing Teeturees S trot Va ro n y EEE SMT Contig ME deerme toa i PVA CH 440744084 oe 193 cis eee amp 1 6e to 1 ot 1 ree eee p Gerah Pratele Ai iprnont s oe Tag Aligpproenta Cet orient or ivtergre trnmoi 7442 Reise threoetine Protein kanasa relata baht MPT erry PFOOOGS GenBank Protein QiLJI0541Ip0LoDIAACOJISOBZ L1 EST Contig oo 05925 EST Contig DA LJ7rL ba BROAD MUU _ 04943 MitLever SCliv ated Or otein nase gos C1 72S or E Gere Ontology Terres Rad a GO Tarn Fungal Anatory F ae xu JR Staiger C1 Mamer Jf iInectivelvicn Of the OWloGern activated protein hinese Mogi from the rice Digest fungus orevents oeretretion of host celis but alps activation of piant defense respo Proc Natl Acodd Sei S A 1998 Octiosrea FIER
9. AAGLAACCE TTT CLC AACACT CPPCC GAAC OCCAACOCOGA TOCOECIOGACCTICICEATCOCAT OC TOGO TICGACCOCICATCCCOTATCTOOOTTOAGCA oC TTC ACI CACECEITIATCOTE CAC ATT OOCALC GATE T OC TAC AACA CTOSOOCOCACCACCTTICAACTICCIACTTITCAA HOT OCOVCGAGGAC OT TOGIGAGATOCOCAAGATGATCCOPTOGACGAGCOTCTACCOTTICOOMCAGCTTOTOcocaccoccccrTe GTaCTOGOGTOOCCACOGTOCACCCCACOCTITCCCCACGOGTOCCOGATCCCTOCACGOGTOCCOGTCAACOGTCAA TOUMSIAACICICCCIACHIA COC GOCEC COOCAAGCGACTAC COT CECT CAGATGAATGACLC TFTAGACOC TGACC TT OCT GOCOSTTIIGGATC AGLACCAGCOTECA MPS OLOGee lev woh IVE CRT TY THE LGOGAYGIVCAAVNNQOTSE OVA RW TN YO Se MILAM RAL BOI LLP ere oerenircure MOIPRAPONFPNETYLYEELMECDLAALRDBDOQPFLTDANP QORP EV CQL COIL EV EMR ANYL HERO KFPUNLE VNADC EL KICOPCUMAROFAYVD Tronsisted Secqwerece PP VAST VV AT FRA HEA EE EET OA EE HE EL AL GGRAPFFKGADODYVYVDODOQOLNOI AHIL GTO PE OTL SeaIGSERAQU YY OPEL PP PASE FT LEON ANP ALIOLL OR MLAP DFR MEIN VE CALL HEV LEEW DADROOED FPOCHT TP NF DFE VVE OVO MERAMILoOoEevy PRP ORCL VIET APR ACES EA PHA PVE FPA ACEHE POW KAR OF REQ YVECMNE PAT LAGGE OOM D Gene Comments Figure 4D In this field you may insert short comments about the gene for example information about its regulation or localization eg upregulated during appressorium development nuclear localized etc Add information as described in Step 5 above E Secreted protein Figure 4L The secreted protein information is generated here by automation using reference e fungi a data resource for compara
10. AT Search Results BLAT SEARCH RESULT BLAT parameters t dna q dna minMatch 2 minScore 30 minidentity 90 maxGap 2 dots 1 out axt Loaded 41643240 lett Searched 269 b i BLASTN 2 2 11 blat Reference Kent WJ 2002 BLAT The BLAST like alignment tool Query sequence 1 2691 letters Database ee a ee ee Lib Yriceblast fasta 41 643 240 total letters searching done score Sequences producing significant alignments bits celeste Figure 13 BLAT result screen will appear Figure 13A Click Retrieve exon positions This will link to copy the new coordinates for the exons back into the transcript maintenance screen Figure 11 The alignment results of the query sequence and the genomic sequence will appear on the same page Close the BLAT result screen The transcript maintenance screen should now have the correct exons and corresponding translated sequence Displayed at the bottom of screen Figure 11B Than click save button to save it on the screen If the desired gene model is not achieved one can go for following steps Figure 11C If there is problem in the number of exons that are required to be in the sequence that can be set by putting values of nucleotide sequence number in the boxes namely Relative start and relative stop provided on the top of the transcript editing page Figure 11D Only required boxes should be kept The delete button can delete as if some sequenc
11. COMMUNITY ANNOTATIONS USER MANUAL This manual is intended to explain in detail how researchers can enter the MGOS database and in particular how to add manual annotation information to the Magnaporthe genome We hope it will stimulate researchers to add their sequence expression and mutant data to provide maximum utility of the information to the community Table of Contents A General Information about Database 1 Information 2 Forum 3 4 IRBC abstracts 4 Gene 5 EST contig 6 RL SAGE 7 Microarray 8 Mutants 9 Genome 10 BLAST 11 BLAT 12 Literature 13 Links B Step by step guide to add annotation information 1 Registration 2 Login 3 Forgot your Password 4 Annotation of a particular locus 5 Entry on Gene page 6 To add information 7 Sections of Gene page A Gene Symbol B Synonyms C Gene Description D Gene Comments E Secreted protein F Gene Ontology Terms G Fungal Anatomy Terms H Publications 1 Add a citation 11 Edit a citation I Mutants 1 Add a Mutant 11 Edit a Mutant J Transcript annotation A General Information about Database For access to the community annotation feature of the M oryzae genome one goes to the MGOS database home page http www mgosdb org MGOS is divided into several subheadings The First section includes Information of general interest about the MGOS project and to the Magnaporthe community 1 Information This contains a
12. cid anion inserted for the GO term will be saved Only one reference can be cited per GO term If you have another reference that you wish to cite for the same GO term you will have to repeat the above process If you have made a mistake and need to start over click on the Cancel button and none of your Gene Ontology information will be saved Please note The Gene Ontology is a work in progress If there are terms that should be defined but are not listed please contact Anupreet kour akjosan email arizona edu or Kevin Greer kevin agcol arizona edu they will assist with updating the ontology G Add a Fungal Anatomy Term Figure 4F The approach here is similar to the Add a GO term section Clicking on the Add a Fungal Anatomy Term link Figure 4F will direct you to a search page Click Choose Term in the Fungal Anatomy Ontology Term row enter the anatomy term you are searching for eg hyphae and click Find Terms This will retrieve a page similar to that in Figure 8 below Click on the appropriate term The next page will display the term its definition and the path to the definition 1 e more general or specific terms If this term is appropriate click Select this term You will be redirected to the search page with your term listed in the Fungal Anatomy Ontology Term field Next add the citation that supports the Fungal Anatomy term either using a PubMed ID or by manually inserting it into the Publication field
13. ck on delete button It will not save the assays in the window After adding the assay one need to click on save button Figure 10F to finally save the assay on this link 11 Figure 4J Edit Mutants already in the database If you want to make changes in already added mutants than you can click on the pencil just near the mutant as shown in Figure 4J and make changes to the fields described above in 4 J Transcript annotation BLAT option is used to annotate the transcript of a particular locus Go to the annotation screen for the locus as shown in Figure 4 Figure 4K Click the pencil that is next to the transcript diagram for the locus to get to the transcript maintenance screen Figure 4K etc Figure 11 The transcript annotation page will appear Figure 11A Click the BLAT a transcript sequence link This is next to exon button Figure 12 It will open a new window for BLAT Than paste the new sequence either EST or Genomic sequence into the top text box make sure to overwrite or delete the sequence that is in the box Figure 12A Click the run BLAT button Different parameters to run BLAT can be selected on the same page under BLAT options Figure 13 Figure 13 home gt AGCoL Gene Details gt Annotation for MMGa0vse2zi gt Gene ic ee Term for MMGa0S621 gt Find Gene Ontology Term for MMGa0se271 G Ontology T f MMiGcats621 gt Add or Annotation a Mutant gt Transcript for MMGa0v0se21 gt Blat CET Page gt BL
14. e is having two exons than except these two exon boxes all the other Figure 11E To set transcript coding sequence the relative values of start and stop codon can be put into the CDS start and CDS stop boxes available Figure 11F After putting these values click on validate button The final amino acid sequence will appear at the bottom of the page Figure 11B These changes can be saved by clicking on save button
15. ed using the MGOS forum by MGOS Admin General Discussion October 08 2007 05 14 49 AM Discussions on various topics concerning Magnaporthe grisea and its interactions in COGEME database links with Oryza sativa by dmsoanes MGOS Comments and Suggestions ogg nai Comments and suggestions related to the MGOSDB website and forum by Ebbole E The Second section of the database contains the DATA divided into several sub sections 4 Gene Following this link opens up gene search page which is the primary page for selecting genes for manual annotation and for viewing features of genes of interest On this page you can search for individual Magnaporthe oryzae locus either by entering an MGOS number MC xxxxx or the associated Broad number MGGxxxxx Moreover a locus name can be written in the Basic Gene Search window 5 EST Contigs Allows searching of ESTs from libraries prepared under several different growth conditions All ESTs in Genbank are available here 6 RL SAGE This section provides access to SAGE data developed in the laboratory of Dr Guo Liang Wang at Ohio State 7 Microarray Under development 8 Mutants To access information on Magnaporthe mutants generated by NSF plant Genome grant select this link 9 Genome To access the Magnaporthe genome browser select this link The Third section of the database contains search tools to help the community to find and annotate loci of interest access to the Magnapor
16. on field will be populated automatically To reference a publication that is not in PubMed leave the PubMed Id field blank Gene Ontology C choose Term ontoloay Website 0 Term Pubmed Id Authors unspecified C Title unspecified Publication Date Journal Volume Pages Evidence Code Guide to GO Evidence Codes D ee E Cancel providing the evidence code If the correct citation populates the Publication field Figure 6C click the Save button Figure 6E and all the information you have Figure 7 MGOS m Miaa home gt AGCoL Gene Details gt gt Gene Ontology Term for MMGa05621 gt Find Gene Ontology Term for MMGa05621 Find Gene Ontoloc Term for MMGa0S5621 Find Gene Ontology Term Sone OR Browse from a top level term biological process molecular function Figure 8 MGOS Sitemap Figure 8 home gt AGCoL Gene Details gt Annotation for MMGa05621 gt Gene Ontology Term for MMGa05621 gt Find Gene Ontology Term for MMGa05621 Find Gene Ontology Term for MMGa05621 Find Gene Ontology Term Find Terms OR Browse from a top level term i molecular function Term Definition More General More 7 Specific Catalysis of the reaction j s acetylcholine carboxylesterase a tivil molecular_function H20 ag choline acetate Catalysis of the reaction an li _ molecular_function acylcholine hydrolase H20 at choline a activ ty carboxylic a
17. ona edu Full contact information is available at the end of this manual Login Figure 2 To Login enter your User Name and Password and click Login If you forget your password you need to click on Forget your password Figure 2B You will be sent an email to enter a new password Or you can contact MGOS administration for more information 4 For annotation of a particular locus Clicking on the M oryzae community annotation link on the front page will take you to the annotation page as shown in Figure 2 After Login on this page as described above you will reach the page as shown in Figure 3 Either you perform a BLAST search with nucleotide and amino acid sequence to identify the locus of interest Figure 3B or use the Broad or MGOS locus number to search the gene of interest Figure 3A All the instructions for annotation are given on this link 5 Next enter the Gene page by clicking on the locus of interest It will take you to the gene edit page as shown in Figure 4 Show audits 1s the option that will take you to page showing about the annotations regarding that gene which includes curator s name and date of curation 6 To add information The gene edit page Figure 4 below is the link where you begin data entry All fields in green are editable All editable fields will also have either a pencil icon or a green underlined link for entry The original information is shown in black For
18. otated A Gene symbol Figure 4A To add or correct a gene symbol click on the pencil icon insert your information and save it Figure 5 M grisea gene symbols are usually three letters and a number e g MFP HDLI CYP1 etc Please see the article by Yoder et al for guidelines on proper M grisea gene nomenclature Yoder O C B Valent and F Chumley 1986 Genetic nomenclature and practice for plant pathogenic fungi 76 383 385 B Synonyms Figure 4B Alternative names for genes go in this field 1 e mutants identified by different research groups have led to different names for the same gene For example NTHI is a synonym for PTH9 MGOS number MC 09471 and is inserted into the Synonyms field To add a synonym select the pencil icon to open the field Figure 4B insert the synonym and click on the diskette icon to save To add more than one synonym separated each by a space or slash C Gene Description Figure 4C In this field you can add a description of the locus if the function of the gene 1s known For example you could insert the full gene name like pathogenicity locus 9 for PTH9 for HDLI you could enter that it encodes a hormone sensitive lipase Add information as described above Figure 4 MmGOoOS Edit Annotation for gene MC_04943 Loain Siteme home gt Genes gt Edit Annotation for gene MC 04943 Dack Green fields are editable Login Locus MC _ 04943 Last updated by anupreet on 200
19. the literature and links of interest 10 BLAST This link is used to search for a particular locus of interest in either MGOS or Uniprot databases by entering either a DNA or protein sequence 11 BLAT BLAT 1s used to find sequences of high identity and of a minimum length and works faster than BLAST For DNA alignments the sequences must be greater than 95 and at least 40 nt in length and for protein alignments greater than 80 identical over 20 amino acids 12 Literature The available literature in MGOS can be searched using this option 13 Links Additionally useful database links along with other additional resource links are available under this option B Step by step guide to add annotation information There are several steps to annotate a locus 1 Registration a To add annotation information to MGOS you need to register as described above Figure 1 or b By clicking on the main webpage of MGOS there is a link for M oryzae community annotation in front of the gene column Clicking on this link will open the page shown in Figure 2 Follow Figure 2A for direct access to the registration page Figure 2 2 3 Figure 2 Login Sitemap You must first login to add or edit data User Name Password Login B ogi A Forgot your password or Veed to register 2 Se ee for MGOS If you have any questions feel free to contact Anupreet kour akjosan email arizona edu or Kevin Greer kevin agcol ariz
20. tive analysis of fungal genome Cornelia etal BMC genomics 2007 8 426 F Add a GO term Figure 4E Gene Ontology GO terms for biological process molecular function and cellular component are added here along with a reference s When you click the Add a GO term link Figure 4E you will be redirected to a Figure 5 MGOS Edit Annotation for gene MC_15370 Figure 5 nome gt EGR Annotation for gene MC_15370 Back Green fields are editable Login Locus MC_15370 Last updated by anupreet on 2009 02 12 16 13 31 779762 Entrez Gene Link Chromosome Linkage i Synonyms AVR Ata F Gene Description MC_15370 metallooroteinase 834 nt new page headed Add Gene Ontology Term for MC XXXX the name of the locus Figure 6 Click on Choose Term Figure 6A to open a search page which is called Find Gene Ontology Term Figure 7 If you already know the GO ID number you can search using it Another way to search is to put your query in quotes e g cholinesterase activity or DNA damage If you just put these phrases in without the quotation marks the search will return everything that contains those two words but not necessarily in the same phrase thus returning too many GO terms Enter your query and click Find Terms Figure 7A When you find the appropriate GO term and definition that describes the molecular function biological process or cellular component click on that term to select it
21. y Sequence Enter query sequence in field below ATGGCTGCAGAGCTGCGCTTCGACGGCCAGGTCGTCGTTGTGACCGGTGCCGGCGGTGGTCTCGGCAAGGC ATATGCTACTTTCT TT GGTAGCAGGGGAGCCAGCGTCGT CGT CAACGACT TGGGCGGCTCATTCAAGGGAG AGGGTACCTCCAGCAAGGCTGCAGATGTTGTTGTAAACGAGAT CAAGGCCGCGGGCGGCAAGGCTGTAGCC AACTACGACT CGGTCGAGAACGGCGACAAGATCATCGACACAGCCATCCAGGCAT TCGGCCGCATCGATAT CTTGATTAACAATGCCGGTATTCTCCGTGATATCAGCT TCAAGAATATGTCCGACCAGGACTGGGACTTGAT TT TCAAGGTCCACGTCAAGGGCGCCTACAAGTGTGCACGGGCAGCATGGCCTCACT T CAGGAAACAGAAGT ACGGTCGTGTTATCAACACTGCCTCAGCCGCCGGTCTGT TCGGTAACT TCGGTCAGTGCAACTACTCGGCTG CCAAGTTGGCCATGGT TGGCT TCACTGAGACGCT CGCCAAGGAGGGCGTCAAGTACAACATACTCGCCAAC GTCATTGCTCCCATTGCCGCAAGTCGCATGACTGAGACTGTGATGCCTCCTGACTTGCTGGCTTTGATGAAG CCCGAGTGGGTTGTGCCGCTGGTIGCTGT CCT GGT CCACAAGAACAACACAAACGAGACTGGTGGCATCTT E Or Upload Sequence File Choose File no file selected A Run BLAT D Reset Figure 107 This scroll down menu contain different values for a particular assay like for appressorium formation it has values like low normal aberrant etc The value can be selected accordingly Figure 10 Value comment window is for the results of a particular assay One can put different values from the experiments with in a assay Figure 10K Image option here is for adding a picture of the particular assay Figure 102 One can click on save button to save the assay on the window If you have added something wrong or don t want to add the assay you can cli
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