User Manual
Contents
1. 7 A P Pa fa MirrerI 7 fa A va g Mirror Orthogonal B xj Import layout Save Discard ares ZY OG i a4 d Layout the network in Cytoscape e The Layout generated by Cytoscape al Crea i C B iy in we Orte Sources Wet lhe fiie 7 Dorade Pe sasID tas Teterettion Befoni tion Fetoork altaple Pile Iypes 0 Sete i Teat gt Setowkh tree Tob Serwiace Source Interaction interaction Type Target interaction Cw 398 Columa 1 v Oenunrineracoon gt CS dency anh tasin PP a Peston ay eT Sew Q columns in BLUE w De loaded a3 EOGE ATTRIBUTES a te JEE 2y gE Tapen artribones ria 8 m ie BF ditifrportteo at a Tapert Attribetes fre B C Shee Tout Pale Tepert Options f Output the Layout e ih ad ty dt eae from Cytoscape in gml or 5 scp teat u BP Pit 124 CIA xgmml file Bode Antevbutes J Lage Astay betes Re Fim Property Pale Curent Setow Tice os Graphics Coleg 5 0 i BN b load the exported data file E AIN A into Cytoscape 4 RY 4 h o 5 KA AU i Select Column 1 in Source 6 P ARN selector and Column 2 in Hh lak 7 l are A 2 y A u WIN s oes Target selector MR AutoSet Save ard c Data loaded in Cytoscape g Back to SRD click the Import layout button to load the gml or xgmml file Re layout category category graph Click the Set Category Category Layout command in t2. Taner Mongolia AHAH Includes 126 sequen All sequence 1 Links in the C 129 li i the Category 5 x 1T16 1259 1731 1266 Wo 1T33 126T Yes 269 Ho T The main GUI contains several sub windows Number Window 1 Dataset selector 2 Zoom selector 3 Inter category drawing window 4 Current sequence list window 5 Foreign sequence list window 6 Foreign relationship window 7 Intra category drawing window 8 Information window 9 Extra category drawing window First use of SRD Description A drop down menu to select dataset to visualize A drop down menu to set or return the zoom factor used for displaying all graphs Used for drawing category category relationships which depicts Chinese province province relationships in this example since sequences in the dataset come from several different provinces in China Lists all sequence within the current category Gives a list of all related sequences linked to the current category or to the selected sequence Gives the relationship value of a selected foreign sequence in the foreign sequence list window The visualization graph for the current category Dynamically displays the corresponding text information of all generated graphs at a time A floating window to visualize another category related to the current category When the program is first started users will find a Start Wizard to quickly acce
3. Before importing users can define all categories CategoryID and CategoryName in the Set categories and category category layout dialog If so the CategoryID in a Sequence Information script file must be consistent with that defined before Users may also define no categories before If so the categories will be defined automatically according to the categories each sequence belong to from the Sequence Information script file 2 When importing new data if a Data set ID DstID a user inputs already exists in the system the previous dataset will be overwritten And the system will ask the user if he want to do so 3 To visualize new data please click Delete all categories command in the File menu to delete all previous data and then import new data Intra category graph drawing An intra category graph is used to depict all sequences and their connections within a category the current category Unlike some regular graph drawing software in which the location of an object is fixed SRD provides an interactive dynamic drawing by using a hot spot technique jointly with a user steered object location Figure 7H A Categories Map and the categoriy hot spots on it 5 p orero T gE M i Guizhou 5 sequences fain rr _ w K una ht a Fh y a F ee Hongkong k The Nansha Islands ly Categories are displayed graphically as a user defined beautiful picture Categories Map in
4. macroscopic understanding of sequence relationships Figure 13H The foreign sequence list is altered automatically when a sequence with SID 133 is selected by clicking the corresponding vertex in the intra category drawing window or clicking the corresponding item in the current sequence list window Virtual C Foreign SID Lae lad 135 12 Extra category graph drawing Continue with the previous section when a user sees several red lines in the inter category drawing window hot spots of all linked categories are assigned a new functional property With mouse moving onto the hot spots users will find that the ToolTip has been changed by being added a new line of text Right click to depict sequences in related category which can not be found on normal category hot spots If a user right clicks one of them the extra category drawing window will be animated from small to big to become visible in the main GUI The animation indicates the opening of the right clicked category An extra category graph has been generated in this window in which sequences and the relationships between them in the right clicked category are illustrated just similar as that in an intra category one This is a particularly important point for interactive graphic displays which is useful for a user to visualize the detail foreign sequences and relationships in another related category Figure 14H Hot spots of all linked categor
5. the inter category drawing window The picture has a hot spot for each category which is also user defined When a user clicks one of these hot spots the corresponding category becomes the current category and SRD displays all the sequences of the category and their connections simultaneously in the intra category drawing window In intra category graphs each sequence is represented by an open circle except for the virtual ones which are displayed as black solid circles The number marked in the middle of the circle denotes the SID of each sequence For clarity only SID is printed in graphs other properties such as SeqID Caption sequence strings etc are not printed However full details are available in the current sequence list window On the other hand SRD provides a hot spot for each sequence vertex When a user s mouse moves onto a vertex circle the mouse pointer changes to the pointing finger shape and the cursor returns the SID SeqID and caption of the corresponding sequence in a ToolTip text box Figure 8H An intra category graph generated by SRD Guizhou DestID total Mumseqs 5 165 4626 6517 1998 The reticulate relationships between each pair of sequences are displayed as connection lines labeled with the relationship values at the middle of the line The minimum and the maximum relationship values are calculated and the corresponding connection line is drawn as red color and blue color res
6. AG A AAMAGTATAC CTCTAGGAC ICAGGGCAS GCATGG TAT AC AAC AGG AC AAA TAT AGI AGA TAT AAT AC AAG AC AT TG Tako T Tats TA A ACHA AA TOSGATAAcACTTTA adt cA CATA TG adda TT Aas fh GAaldalTTggg aac AS A AAT AA tI TT AatCladTCT TCsAGcGAGGGG ACCC AG AG ATTG TAATGCACAGTITTAaTIGO GS GAGGGGAATTTITIC TACTSTAATACATCAcKaC TG TTTaatagtacttggaatggtac tagt acttggaat ivatactacaggaaatagcACtATcAC G CTITCCCTTGCAGAATALAACAC ATTGTAAACATG TGGCAG GALGT 4 GGG AMAGCCA ATG TATGCCCCTICCCATT aGacGs cA sATTAcs TGOTTcATCA AATATT ACA GGGTTG CTATT AAC AAG AG ATG Tot T AAt At GA AG cat T A cA ot 4G ACCTTCAAS CCT eGGAGGA GG gt 156 TL 5693 7616 0 1998 TAG TAC Ag TTC AStG AAT CTG TAG T AAT Tat To ae ate OC ea eC TAC AACA BAA AC TATAC cTCTAGGAC CAGGGCAA GCATGOTATACAAT AGGA CALATAATAGGAGA TAT AAS AC AAC AC AT TO Taal T TAG Tag a0 a a TGGGATAAcACTTTA ad ca GATAAcTG ads ATT Ade t FAaldalTTagg aacht A AAT Ad t I TT AatCladTCT TCs AcGAGGGGACCCAG AG AT TG TAATGOCACAGTOTTAATIGONS GAGGGGAATTTTIC TACTGTAATAC ATC AcdaC TG TT Taatagtacttggaatgataa tagt acttggaat jaatactacaggagatagcAdtATcaAC G CICCCTTGCAGAATAAAACAA ATTGTAAACATG TGGCAG GAALGT J4 GGG AAAGCA ATG TATGCCCCICCCATT aGAGGA chad T TAgt TGIIcCATCA AATATT ACA GGGTTG JadGa AT s AG aAC el eg AC CAC cb E reece LOT IL 5694 Ta17 0 1998 TAG TAC Ag TIGAAtGAALCTG TAG AAAT TAMt TG TAC aAG A CCCAACAACAATACAAGA AAAACTATAC aTCTAGGAC The category each seque
7. AGCTACT TEGARTGATACTACAGCCAAATAGCAATATCACECTOCCTTECAGAATARAACAAATTGT si AAACATC TEE CAGGAAG TACCCAAAGCAATETATOCOCCETCOCATICOACCACAAAT TAGATETTICATCARATATTACAG sq GCETTECTAT TAACAAGAGATEGTEGTAATARTGAGAARCAAGACCACCGAGACCT TCAGACE TEGAGGAGE SH 155 5492 7615 Uir Ho 1998 sq TAGTACAGRCTCAATOCAATE TOC TAAABAT TAATTOCTACAAGACCCAACARCAATACARCAAACALTATACCTETAGCCACEA ELI CECARACCATGGTATACARAACADCACAAATAATACCACATATAACGACAACCACATTETAACET TAGTACAACACGAATDEAA ELI TAACACTTTACGAAAAGATAACTCEAAAAATT ACAGCAACAATTTEACAACAHAAACAATARATETTT RATCAATCTTCAREGAG sq CECACETACAGAT TOARATCCACRETTT TAATTETCCAGGEEAATTITTICTACTETAATACATCACAACTECTTTAATAGT Si AE TIEGAATEATACTALTACTICCVLAATOATAATACALLAAATDACARTATCACGE TEC TI OCALAATARALCAAAT Tit 3 AAACATETERCAGEAAG TAG GEG AAAGCAATETATGCCCCTCCOCAT TGAAGEACAAAT TAGATET TCATCARATAT TACAG sq CET TECTAT TAACAAGAGATEETEGCAT TAATGAGAECGAGACCACCEAGCACCTICATACCAGCAGGAEGE SH 156 S699 7616 Uir Ho 1998 si TAGTACACCICAATCAATETOTACGTAATTAATTETACRACACCCAACAACAATACAACARAAAGTATACTEIRCECADCCAG ELI CEARAACATEGTATGCCARCAGGACARAT AAT AGG ARATATAAGACAAGCACATTGTAACAT TAG TAGAARAGCTIGGAAT sq AAAAE TT TACAACACAT AAC TARAAAAT TARGACRAC AAT TI COCARCARARCAATAATETT TAAGCAACE TC TIT CEAGG ai ACCECACCCACGACATIETAATEOCACACETTTAATTETECACCOCCARATITTITETACTETRATACATCACAACTETTTAATA ELI GTACTIGGAATFATACTAGTECT TGGAATGATACTACAGGAAATGACACTAICACGCTCCCTTGCAGAATAAGACAAATTI sq CTARACA CCT ECACC AAG TACC CARRE CARTE TATCCCOCTOCCATTAGCAGGACTARTIAGCATCTIGCATCARATAT TAC ACE
8. LE TIGL TATTARCAAGAGAT CE TGG TET TART OAR AC CAAT RAT ACCA ACRE TTC ADR Th CALEAGG Su 157 5694 7617 Uir Ho 1998 sq TRE TACAGCTGAATEAATCTETAGAAAT TARTTE TAC AAGACCCAGCARCAATACARGARAAARETATATCTCTAGEACCA sj aa A a aaa LLL cy b a A text file generated by SRD is composed of different types of lines Types of lines Description DD Current dataset ID DstID CM Comments DT Date and time when generate this file CG Current category SH Sequence header a sequence description followed by lines of sequence data SQ Lines of sequence data LS The links is related to all sequence or to the selected sequence 21 LH LK Link header a link description followed link information Link Information including the pair of two sequences with their relationship value End of file 22
9. SRD User Manual Table of contents 1 Overview 2 First use of SRD 3 The Sequence Information Script File format 4 The Sequence Links Script File format 5 Import new data to visualize 6 Intra category graph drawing 7 Category Category graph drawing 8 Extra category graph drawing 9 Recursion extra intra categories 10 Fully customizable interface 11 Categories definition 12 Set Categories Map 13 Re layout objects in each intra category graph 14 Re layout category category graph 15 User defined help document 16 Splitting sub windows in different views 17 Results Export Overview SRD Sequence Relationship Drawing program was developed in order to dynamically draw plane undirected graphs for a wide range of sequence relationship visualization analysis either for nucleic acid sequences or for peptide sequences Categories analysis is also supported which allows visualizing intra category sequence relationships extra category sequence relationships and category category relationships in several specific windows respectively The following picture is the overview of SRD main GUI window The sample dataset used here is a dataset of China envelope glycoprotein env gene of HIV sequences derived from Chinese center for disease control and prevention Figure 1H The main GUI of SRD J Sequence relationship drawing File Edit View Help Bae o bolle 9 wo a e a agau i Qinghai
10. able and selectable when an item is selected the corresponding vertex in the graph will be highlighted automatically and the drawing window will be scrolled if necessary to make a view of 10 putting the vertex circle in the center This is very useful for a user to find out the vertex of a specific sequence in the graph from the detail list Figure 10H Details of sequences within the current category are list in the current sequence list window PeR E025 Sea e Se Sc See E 5691 7614 TAGTACAGCTGAATGAATCTGTAG z PS Tiin 5692 7615 Mo 993 TAG TALAGCTGAATEAATCT GTA ee 156 Jilin FBS 616 No 1998 TAGTACAGCTGAATGAATCTGOGTAG AE 157 Jilin pEg4 761 Mo 1955 TAGTACAGCTGAATGAATCTGTAG 2158 Jilin 5695 7618 Mo 1998 TAGTACAGCTEA4TEAATCTGTAG gt Category Category graph drawing The intra category graph shows sequences and their relationships within one category Another undirected graph is provided in SRD in the inter category drawing window with each category as a vertex to depict category category relationships The category category graph is somewhat different from the intra category one although both of them are undirected graphs Firstly the fact that a category linked to another only denotes that there exists some relationships between the sequences within the two categories so we needn t define a category category relationship value and therefore no value will be labeled on the connection lines i
11. e and can be dragged to anywhere in the main GUI of SRD It can be closed at any time by clicking the close button at the top right of the window Animation is used again when the window disappears as it returns to its corresponding category Recursion extra intra categories As mentioned above it is easy to view category category relationships and to generate an extra category graph However although clicking a sequence in an extra category graph can control edges displaying separately there is no effect on category category relationships and foreign sequences which is different from selecting a sequence in an intra category graph This is 14 because there can be only one current category at a time and category category relationships and foreign sequences are relative to the current category But sometimes one may concern about the category category relationships and foreign sequences relative to the extra category rather than current category when he is looking at an extra category graph The proposed software adopts an extra intra category transferring technique which have combined these three perspectives to create a highly integrated multi window visualization in the SRD environment This can be simply done by another mouse action double click A double click on one vertex in the extra category graph leads to a current category transferring The extra category drawing window is animated fro
12. es in this example Seq 1 Seq 2 Seq _3 are Sequence ID and RANDOM 4954 RANDOM 5537 are captions in this example p The separator I can also be lt Tab gt like the following example cl seg 1 RANDOM 4854 cl seq 2 RANDOM S537 2 ce seq RANDOM lhe ce seq 4 RANDOM 6625 gt ca seq 5 l RANDOM e121 In this example we omitted the sequences And a sequence Virtual or not is given 1 presents virtual O presents not The sequence ends if another line starting with a gt or end of file EOF appears The script file is text based and can be created and edited using any text processing tools or by simply pasting from some other software tools such as Excel Orgin Pro or Matlab Note that text pasted from Excel is separated by a lt Tab gt character It can be imported directly into the system by the Import New data dialog provided by SRD which is activated by mouse clicks throughout the entire importing process An input module of the software will automatically detect the file formats and an internal syntax analyzer will give back any error information When the input process completes the parser recognizes the text and stores all the information into the background database along with the application The Sequence Links Script File format Users must create a Sequence Links script file that contains relationships between each tw
13. gory category map click Set Categories Map command in the File Menu Choose a picture as the map Any picture with bmp jpg gif format is supported In the example we choose a China map as the category category map because we partition 15 all the sequences to several Chinese provinces Re layout objects in each intra category graph Click Set Intra category layout command in the File Menu to open Set intra category graph layout dialog Then choose the dataset DstID and the category in the two drop down menus bellow The dialog presents the sequence list in the selected category and illustrates the undirected graph to users graphically All objects coordinates can then be adjusted by loading layout files generated by other tools or by user s mouse dragging in this graph Click save button to save all the changes to the database Figure 18H gives an example of dragging objects to set layout Figure 19H gives an example of import layout generated by Cytoscape Set intra category graph layout IstIL HIY Category aH 10 a 38 1TS1 1266 2005 Z links in the category Drag to change position right click to show only rela A oF in Export Objects Import Layout r Autoset Save Discard Po 16 File Edit Select EOL Rotate DRAE sa Tie Conto Panel Alig d Distribete p Setocrk Vittapper Settings Setocrk Joragh layset
14. he File Menu Select a category in the list at the right of the dialog displayed Then click mouse at somewhere in the picture map at the left to draw a proper circle to set the hot spot range for the category 17 Figure 20H Set hot spots for categories It is setting a hot spot for category Guangxi in this figure Set categories and category category layout E E User defined help document SRD allows importing a user defined available RTF Rich Text Format file into the system as a help document in which information appears as color coded text The RTF file can be generated by most word processing software such as Microsoft Word Windows WordPad Open Office etc and saved as a RTF file The RTF format help file can then be further imported using the Import Figure 21H A Help document displaying as RTF format Help document oO x Sequence relationship drawing Help Document The Help Document is meant to be a very basic guide to help Please edit your om help document by a word processing software save az RIF format and click help import help document to import it to the system 18 help document function in the help menu The help document can be displayed in another window by clicking the help function in the help menu or press Ctrl F1 Splitting sub windows in different views The main GUI of SRD composed of several sub windows Users are enabled to drag the co
15. ies are assigned a new functional property Zory An extra category graph has most the same characteristics as an intra category one such as circular vertices connection lines hot spots etc Sequence vertices are also clickable to draw connection lines separately A special characteristic of an extra category graph is that vertices of all foreign sequences in this graph are filled with a particular color which denotes that there are some relationships between them and the current selected one Furthermore SIDs of related sequences and relationship values can be displayed in the prompt ToolTip text when mouse moving onto the foreign sequences vertices which allows a user to quickly get the information about which a colored sequence is linked to and how about the relationship values Alternatively another way to open the extra category drawing window is to click one of the 13 Figure 15H An extra category graph Guizhou DetID total Mumseqs 5 items list in the foreign sequence list window In this way the drawing window will scroll Figure 16H Cursor gives the linking information when mouse moves onto a foreign sequence vertex Guizhou Det D total Hurmsegs 5 166 48285 6517 1998 Links to the sequence 137 value 2045 in cluster Henan Mouble click to show outer cluster links automatically to make the selected sequence into view Moreover this window is a floating window which is always placed abov
16. m big to small again but to disappear at the middle of the intra category drawing window which indicates that the current category now has become the one previously in the extra category window The double clicked sequence is then automatically selected in the now intra category graph All other windows are changed according to the new current category and the new selected sequence One may right click a related category again to open the extra category drawing window and double click a sequence in this window to make a second extra intra transferring Then right click another category and transfer again This recursion is helpful to trace a sequence relationship path between different categories especially in investigating a revolutionary path between different organisms or investigating a disease transmission path between different places Fully customizable interface To cater to the broadest array of biological scientists users the program is fully customizable for categories definition category category map picture all vertices locations and even help document Categories definition To make categories definition click the Set Category Category Layout command in the File Menu A category list will be shown at the right bottom in the displayed dialog Click the Add or Delete button to add a new category or delete the selected category in the list Set Categories Map To customize a cate
17. mmon border of each two adjacent windows to resize each other If the dragging horizontal border up and down or dragging vertical border left and right the border s orientation can be changed from horizontal to be vertical or vice versa This can be used to re arrange the sub windows layout of SRD Figure 22H a Drag border to resize sub windows and re arrange windows layout J Sequence relationship drawing a 3 O x File Edit View Help Be So RESO av ooo AHAH Includes 126 sequence ls All sequence links Links in the Category 129 links in the Category 19 Figure 22H 6 The border can be draged from vertical to horizontal to re arrange windows layout J Sequence relationship drawing File Edit View Help 1191 99 1193 99 oo F Ee e AHAH Includes 126 sequence ls All sequence links Links in the Category 129 links in the Category Figure 22H c A new re arranged sub windows layout Sequence relationship drawing O x File Edit wiew Help k ESIL BEL oO HIY Tibet L 1H g p F in pE So A 1187 989 Ho 2005 1191 991 Ho 2005 y a q AHAH Includes 126 sequence s All sequence links Links in the Category 20 Results Export Finally for the purpose of input to other applications or the purpose of further analysis the capacity to output results is essential The output layer is able to directly write contents in all lis
18. n sequence list window Foreign SID Category Seq Virtual Caption Sequence Memo _ oe 34 AH 1385 10385 Wo z005 TAGTACTA 50 AH 1456 1143 Wo z005 TAGTACTA 70 AH 1576 1167 Ho 2005 TAGTACTA JA 119 AH 1616 1508 Wo z005 TAGTACTA ey 142 HA 1039 6738 Ho 1996 TAGTACTA ee 155 JL Egz TE1S Ho 1998 TAGTACTA Figure 12H 6 Related sequences and their relationship values of the selected foreign sequence will be shown in the foreign relationship window right 1305 1098 H 1456 1143 H 1576 1167 H 1816 1308 H 1039 6138 we a There is also a mechanism to get extra connections separately 1 e to get extra connections only linked to the selected one sequence in the current category rather than all of them This can be simply done by selecting one sequence by clicking on the corresponding vertex in the intra category drawing window or clicking the corresponding item in the current sequence list window As mentioned in previous section this will lead to the selected sequence vertex to be highlighted and connection lines displayed separately in the intra category graph At the same time this will also affect extra connections Category category edges and foreign sequence list will also be altered automatically according to this selection Once again how extra connections are displayed depends on a user s selection Combining this feature with intra category graph provides a
19. n the category category graph Moreover when drawing an intra category graph to illustrate sequence relationships within the current category at a larger scale the user will want Figure 11H A category category graph Heilongjiang f U Gadi A c a y aral ngkong Wiacan gt ner Wy The Nansha Islands i to see whether and how her current category are related to someone else At this scale in the category category graph it should be straightforward to display edges that only linked to the current category while other edges should be omitted at the moment for clarity In SRD when the current category is selected by clicking the corresponding hot spot in the Categories Map an intra category graph is generated and simultaneously edges linked to the 11 current category are displayed as several red lines in the inter category drawing window At the same time the foreign sequence list window 1s also filled with some sequences which are called Foreign sequences since these sequences listed here denote that each of them is related at least to one of the sequences within the Current Category The relationship values can be shown in the foreign relationship window when a foreign sequence is clicked in this window It is useful to get a detail list of related sequences in other categories while visualizing an intra category relationship Figure 12H a Foreign sequences are list in the foreig
20. nce belongs to must also be given by a string identifier a string not more than 50 characters which is called CategoryID The field SeqID can be the name or the database ID of the sequence e g a gi number of NCBI a PDBID of PDB database etc Is Virtual indicates it is a virtual sequence 1 or not O Caption is a text string that describe the sequence could also be none Other corresponding information can be included in the field Memo Another example with SID being omitted of such file is as follows gt el Seq_1 RANDOM 4954 CTCAAGAGTACGGCCTCTAGGTCAAACCGTACTTTTTCGTGGTGGATTGATAACTTCGGACGATGTCGCATCAGGTCGTG ATTTTCGTTTGAACGTTTGTACATCATGCGCGTTAGGGAGGTGTGGCTCCTCAACGTTTTCGAGTCAAGTCCCTTCATAG ACGTCCGTCGATCTTATCGA gt el Seq_2 RANDOM 5537 ACTCTCCGTCGAATCAGCTGAATGCAATGTGATTGTGCGTACATTTTCTGAGCAC gt c2 Seq_3 RANDOM 1622 CCCAAACTCCACCAGCCGATTTTTCTACAATTCTCCCTTTTTTGGACATCGGGTGGGGGGCAACCGTAAGCCCGGAATTT GAGGGCGCGCAAAAACCCCGGCACCCGCACC gt c2 Seq_4 RANDOM 6623 CTTGAGCGCCTGCGGTGGAAGAGTAAACCCAATGAATTCCACCGTCCTGATAGTCCTGTCATCCGGACCCCGCGCCATTG AGTC gt c3 Seq_5 RANDOM 8121 TTGTTTAGAGTTTATCCACGCATACTCCGTCGCAAAATTATTGAGCTCCCCTAAGGCCATGCCATCATCCCACTAAACCA ACGTACAAGTGATAGGCATTCCGAAACGAATGTTTGCGAACCC Note that the P character after gt must exist since SID is omitted The c1 c2 c3 is the IDs of the categories which should be no more than 50 characters We partitioned all sequence into 3 categori
21. o sequences Both the script files are text based and can be generated and edited using any text processing tools Sequence Links script file can adopt one of the following format Matrix format a nxn matrix separated by spaces in each line The separator can be one space or several spaces or even Tab which is useful to load a table style text file Figure 4H A sample of Sequence Links script file Matrix format O 1667 O 1TS 0 2046 0 2209 0 2158 eel 2146 2261 e023 1735 lagg 1883 TT 2004 1655 0 194 lata 1698 0 0 0 0 0 0 0 0 0 0 0 1758 0 0 0 0 0 0 0 0 a2 FPRoOUOCOOOOOGOGOO OOO Oooo oo D O D A A A A A A A AA AGAAGA GAA AA A D O D A G AA A GG AA AGA GA GA A AA D O D A A A A G AA A G GAA GA GA A AA E a s as a A a A e A a A mn AA s Ga A a A m A man A a B D O D A A A A GG AA A GA A GA GAA AA AA n e a n A m m AA n A m AE e AA a BA mn GA m AA man E a m AA a A i D O D A A A A GA A A AA A GAAGA GA AA A E m a n a a a A a A e A ma A m A e BA m A n AA ma A m A ma BA o AA a A mn H Z Relationship lines format each line indicates one relationship and its value between one pair of sequences For instance if sequence SID and sequence SID2 has a relationship value V the corresponding line should be SIDI SID2 V The separator can either be a Tab or any number of spaces SID1 and SID2 must be consistent with the ones in the Sequence Information script file Fig
22. on script file adopts a format as a FASTA file that begins with a single line description followed by lines of sequence data The description line is distinguished from the sequence data by a greater than gt symbol in the first column There should be no space between the gt and the first letter of the identifier The description line must exist for each sequence while the rest sequence data lines are optional The as description line must adopt a specific format with several fields separated by a I character or a lt Tab gt character The format of the description line is as follows gt SID CategoryID SeqID IsVirtual Caption Memo Where fields in brackets are optional and can be omitted Each sequence must be assigned a unique zero based identifier number called SID Note that SID can also be omitted and be generated by the system but the Il or lt Tab gt character after SID must exist Figure 3H A sample of Sequence Information Script File 154 JL 691 7T614 0 1998 TACTA CAgTTGAAtGAAtCTCTAGAAATTAAtTGTAC aG ee eT AC Be AAAAGTATACaTCTAGGAC CAGGGCAA GCATGOTATACAATAGGACALATAATAGGAGA TATALGACAAGCACATTGIAACATTAATAg ACADA GFHaldalTT eee aac AAA ar a aT Ae tI TT AatCladTCT TCsAGGAGGGGACCCAGAGATTGTASTGOCACAGTITTAaSTIGONS GAGGGGAATTTITIC JAN ACC TCANS CCT GNAGGA GG 155 JL 5692 7615 0 1998 TAG TAC AgC TG AAtGAAtCTG TAG ASAT TAMt TG TAC aAG A COCAACAACAATAC A
23. pectively This is useful for the user to find out the minimum and the maximum relationship and acquire the value range at a glance Figure 9H Select a sequence and display edges separately in an intra category graph The sequence with SID 197 is selected in this example Jim DstID total Mumoeqs 5 197 S692 7615 1995 When there are a large number of sequences and a large number of relationship links connection lines will mix up together To overcome this problem separate edges displaying is supported in the system Any sequence can be selected by clicking on the corresponding vertex When a sequence is selected the corresponding vertex is highlighted with a particular color and edges only linked to the selected sequence are drawn other edges are omitted The minimum and the maximum relationship values are re calculated and colored lines are also re marked according to the current lines drawn When users click anywhere else of the graph all connection lines will display together again Which part of the edges to be displayed depends on the user s selection Furthermore sequence selection displays synchronously with the current sequence list window When a sequence is selected in the graph the corresponding item in the list window is highlighted and brought into view automatically which is useful for a user to check the detail information about the selected sequence Conversely sequence items in the list window are also click
24. s assign all sequence to one same category 2 This step is optional Manually rearranged the graph for each category by mouse dragging the sequence vertices to make the graphs more beautiful using the Set intra category graph layout dialog In this dialog we also can export objects into a text file for layout by other software tools and import the layout generated by other software tools To open the Set intra category graph layout dialog click Set intra category layout command in the File menu 3 This step is optional To vividly depict different categories create a picture called Categorys Map using any image creation and editing tools such as MS Paint Photoshop Fireworks etc in which each category has an icon on it Import the picture using the Set categories map command in the File menu 4 This step is optional Using the Set categories and category category layout dialog set hot spots for each category on the Categorys Map imported in the previous step You can further add or delete categories in this dialog To open the Set categories and category category layout dialog click Set category category layout command in the File menu Sample datasets are available on the website The Sequence Information Script File format Users must create a Sequence Information script file that contains all sequences and their categories in the dataset Sequence Informati
25. ss general functions in the system Novice users should follow the steps and click the commands in the wizard window to perform their visualization Figure 2H Start Wizard in SRD Start Wizard e Welcome to Sequence Relationship drawing To import your own data to visualize sequence relationships based om undirected graphs please follow up the following steps Hote that only the first step with is required Import sequences and relationships between them inte the system to visualize Set sequence vertex coordinates in each category Set a User Defined picture as a Categories Map in which each category has a symbol icon Set hot spot for each category in the above oordinates picture Step S Further Set Further set categories or add or delete Categories categories W Show this dialog at startup Fold eine Step 4 Set Categories C To begin the visualization 1 In the first step create a Sequence Information Script File to contain all sequences information and their categories Create a Sequence Links Script File to contain the relationship values between each two sequences Import the two script files into the system using the Import New data dialog To open the Import New data dialog click Import New data command in the File menu If one would like to visualize all sequences as a whole i e not perform the partition into several categorie
26. t windows to files copy any graphs into the clipboard and save pictures as BMP bitmap image format files These can be done by a simple mouse right click in most windows of the main GUI and choosing the corresponding functions in the pop up menu To efficiently view the results generated by SRD text output is also supported as complementary to the graphical drawings A text file can be generated to describe current graphs by clicking the Output Text Information function in the edit menu The text file is structured so as to be usable by human readers as well as by computer programs It is composed of different types of lines each with its own format which are used to record the various types of data Some files will not contain all of the line types and some line types may occur many times in another file this depends on the user s selection in graph drawing window A terminator line designates the end of the file Figure 23H An output text file generated by SRD oo HIY CH fy SRO Yer 3 7 oT 2013 31 13 41 03 CE all SH 15h S691 76145 YirsHo 1998 3g TAGTACAGCTGAATGAATCTETAGAAAT TARTTGTGCAARGACCCARCAACARTACAARGARAAAGTATACATCTAGEACCA ig CCCCARCCATEGTATACAACACCACAAATAATACCACATA TANG ACAACCACATICTARCET TRETAGARC AAA TOCA ELI TARLAC TT TARRACACATAACTLRARRAAT AAG ADRAC AAT TGA AR AACA TAG TCT T TAA CAR TET TAA 39 CGEACCCAGAGAT TG TARTECACAGTITTAATTGOTEGAGGGGAATITITECTACTETAATACATCACAACTORITAATAGT aq ACTIGGAATERTACT
27. th the script files using the Import New data dialog To open the Import New data dialog click Import New data command in the File menu Figure 6H The Import New Data dialog Import New Data g E X import sequences information not include sequence coordinates Then import sequence links T Import a new set of sequence relationships Hew DstID Fisrtly Sequence information file format SID must be range from zero to nj gt SID CategoryID SeqID Is irtual Caption Memo HHMEKEREE Gequensces xXXNNEXEXX HHREREREE Sequences HXXHHHXNHH HexntSequence Import links Sequence links file can be a matrix file or adopt the format below SIII SIDS Relationship alue e g 1 2T 0 0545 1 32 0 0247 Close Click Import sequences command to import a Sequence Information script file Then click Import Links to import a Sequence Links script file Data set ID DstID will be asked when click the commands Please Input a string no more than 50 characters as your dataset ID The dataset ID you input must be consistent the same with the two askings when you click the two commands separately When the Sequence Links script file importing is complete graphs layout for all categories will be performed automatically automatically set vertices coordinates of all sequences and data structures will be optimized for fast running Note 1
28. ure 5H A sample of Sequence Links script file Relationship lines format lo 2 0 1687 a lo 5 0 173 lo 5 0 1887 0 7 0 1956 10 id 0 1936 lo 15 0 1678 0 17 0 1701 lo 18 0 2004 l 19 0 1784 1 2 0 2046 1 3 0 2209 1 d 0 2158 4 6 0 2076 1 B 0 1675 1 10 0 221 1 12 0 1673 1 13 0 2096 1 id 0 2139 1 17 0 2201 1 19 219 2 5 2121 2 z 0 2146 2 11 0 2023 2 12 0 2262 2 16 0 2254 The script file is text based and can be created and edited using any text processing tools or by simply pasting from some other software tools such as Excel Orgin Pro or Matlab It can be imported directly into the system by an interactive Import New data dialog provided by SRD which is activated by mouse clicks throughout the entire importing process An input module of the software will automatically detect the file formats and an internal syntax analyzer will give back any error information When the input process completes the parser recognizes the text and stores all the information into the computerized database along with the application Import new data to visualize To start a sequence relationship visualization sequences and the relationship values must be imported into the system Users must create a Sequence Information script file that contains all sequences and their categories in the dataset and a Sequence Links script file that contains relationships between each two sequences Import bo
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