1. HKUHKU Computer Centre Introduction to SRS Frankie Cheung frankie@cc.hku.hk

2. HKUHKU Computer Centre Introduction to SRS Part 0. Introduction

3. HKUHKU Computer Centre SRS Introduction Sequence Retrieval System parsing and indexing  SRS system started out as a Sequence Retrieval System that employed sophisticated parsing and indexing of database text files

4. HKUHKU Computer Centre SRS Introduction  Fast access  Fast access to diverse life science data - genetic, protein, cellular, molecular, and clinical - for researchers and bioinformaticians one interface  Integration of public and proprietary data through one interface cross-database queries  Unique ability to perform cross-database queries  Rapid string search  Rapid string search of large volumes of data integration of data and analysis tools  Seemless integration of data and analysis tools

5. HKUHKU Computer Centre Starting SRS  Browse the BIOSUPPORT Hompage: http://bioinfo.hku.hk/ http://bioinfo.hku.hk/ “Tools”  Select “Tools” Option

6. HKUHKU Computer Centre Starting SRS Sequence Retrieval System (SRS)  At the “Tools” page, find and click on the Sequence Retrieval System (SRS) system

7. HKUHKU Computer Centre SRS Main Page Temporary Project  After successful login, the default page is a “ Temporary Project ”.

8. HKUHKU Computer Centre SRS Main Page Temporary Project  For a “Temporary Project”, the result of your work would not be stored after you close SRS.

9. HKUHKU Computer Centre SRS Main Page Permanent Project  Starting a “ Permanent Project ”, the result of your work would be stored even after you close SRS.

10. HKUHKU Computer Centre Permanent Project Permanent Project  After selecting a “ Permanent Project ”, your account name and project name will be displayed. (Since no password protection under current policy, this approach is not recommended.)

11. HKUHKU Computer Centre Permanent Project Permanent Project  All the query and job result will be saved in your “ Permanent Project ”.

12. HKUHKU Computer Centre Permanent Project Option Save to desktop  “ Save to desktop ” : download & save your project info to your local machine

13. HKUHKU Computer Centre Permanent Project Option Rename project  “ Rename project ” : change the name of your project

14. HKUHKU Computer Centre Permanent Project Option Delete project  “ Delete project ” : delete all the related information of your current project

15. HKUHKU Computer Centre “Quick Searches” page :  Quick access with default databank selection

16. HKUHKU Computer Centre “Quick Text Search”  Quick sequence query with default databank selection  Enter your search string and click “Search” to start searching

17. HKUHKU Computer Centre “Quick Text Search”  Default Databank Setting: Nucleotide SeqEMBL Protein SeqSWALL Protein StructurePDB GenomeLocusLink MutationsOMIM Metabolic PathwayPathway

18. HKUHKU Computer Centre Introduction to SRS Part 1. Simple Query

19. HKUHKU Computer Centre Simple query Select Databank PIR  Go back to “ Select Databank ”, click on “ PIR ” to select “PIR” databank

20. HKUHKU Computer Centre Simple query Query  Then click the “ Query ” button to fill in the query form

21. HKUHKU Computer Centre Simple query AllText Description  Click the first “ AllText ” pull down menu to change it to “ Description ” cytochrome  Enter “ cytochrome ” at the blank besides

22. HKUHKU Computer Centre Simple query AllText Organism  Click the second “ AllText ” pull down menu to change it to “ Organism ” pig  Enter “ pig ” at the blank besides

23. HKUHKU Computer Centre Simple query Search  Click the “ Search ” button to start searching any sequence in PIR databanks satisfy your query form

24. HKUHKU Computer Centre Simple query  After searching for awhile, there would be some result listing entries. PIR:S26019  Try to click the PIR:S26019 entry

25. HKUHKU Computer Centre Gene Sequence ID, accession number, description, keywords  SRS would display the PIR:S26019 description: including ID, accession number, description, keywords, etc

26. HKUHKU Computer Centre Gene Sequence Medline reference  Scroll down to see the reference related to this sequence, there is also a Medline reference hyperlink available

27. HKUHKU Computer Centre Gene Sequence gene function gene sequence  Scroll down to see the gene function and the gene sequence

28. HKUHKU Computer Centre Gene Sequence  Save the gene sequence information to your local machine Save  Click the “ Save ” button at the leftmost panel

29. HKUHKU Computer Centre Gene Sequence Output to  Click the “ Output to ” button to choose the text/html format

30. HKUHKU Computer Centre Gene Sequence Complete entries  Click the “Use View” button to choose the “ Complete entries ” format

31. HKUHKU Computer Centre Gene Sequence save  Then click “ save ” to save again the PIR:S26019 to your local machine

32. HKUHKU Computer Centre Simple query: Exercise 15 Minutes Break Please try the following exercises by yourself!

33. HKUHKU Computer Centre Simple query: Exercise Question 1.  Search all the “SARS virus” in EMBL databases

34. HKUHKU Computer Centre Simple query: Exercise  1. Search all the “SARS virus” in EMBL databases

35. HKUHKU Computer Centre Simple query: Exercise  1. Search all the “SARS virus” in EMBL databases

36. HKUHKU Computer Centre Simple query: Exercise  1. Search all the “SARS virus” in EMBL databases:

37. HKUHKU Computer Centre Simple query: Exercise Question 2.  How many CDS regions for the “EMBL:AY278488” (SARS coronavirus BJ01) ?

38. HKUHKU Computer Centre Simple query: Exercise  2. Click to see the detail AY278488

39. HKUHKU Computer Centre Simple query: Exercise  2. Click to see the detail AY278488

40. HKUHKU Computer Centre Simple query: Exercise  2. Count the number of CDS entries

41. HKUHKU Computer Centre Simple query: Exercise  2. CDS entries of EMBL:AY278488  orf1ab  orf1a polyprotein  spike glycoprotein S  putative uncharacterized protein 1  putative uncharacterized protein 2  envelope protein E  membrane protein M  putative uncharacterized protein 3  putative uncharacterized protein 4  nucleocapsid protein N  putative uncharacterized protein 5

42. HKUHKU Computer Centre Simple query: Exercise Question 3.  What is the protein ID for EMBL:AY278741 (SARS coronavirus Urbani) spike glycoprotein?

43. HKUHKU Computer Centre Simple query: Exercise  3. Click to see the detail AY278741

44. HKUHKU Computer Centre Simple query: Exercise  3. EMBL:AY278741

45. HKUHKU Computer Centre Simple query: Exercise  3. EMBL:AY278741

46. HKUHKU Computer Centre Simple query: Exercise Question 4.  Following the link of the spike glycoprotein of EMBL:AY278741, what is the biological function of this spike-protein?

47. HKUHKU Computer Centre Simple query: Exercise  4. EMBL:AY278741

48. HKUHKU Computer Centre Simple query: Exercise  4. Find biological function of VGL2_CVHSA

49. HKUHKU Computer Centre Simple query: Exercise  4. Find biological function of VGL2_CVHSA

50. HKUHKU Computer Centre Introduction to SRS Part 2. Extended Search

51. HKUHKU Computer Centre Extended Search Select Databanks  Click the “ Select Databanks ” button at the top to select PIR as query targe

52. HKUHKU Computer Centre Extended Search Query  Click the “ Query ” button at the top to back to query form

53. HKUHKU Computer Centre Extended Search Extended Query  Click the “ Extended Query ” button at the left panel to display the extended search form

54. HKUHKU Computer Centre Extended Search Extended Super Family cytochrome-c  In the “ Extended ” search form, find the “ Super Family ” field and then enter “ cytochrome-c ” Search  Click the “ Search ” to start the query

55. HKUHKU Computer Centre Extended Search  After searching for awhile, there would be extended search result list appear

56. HKUHKU Computer Centre Using Search Results Result  Click the “ Result ” button at the top to reuse your query result

57. HKUHKU Computer Centre Using Search Results Q1 !Q3  In the “Result” pages, enter “ Q1 !Q3 ” at the top blank field and click “Expression” to combine 2 queries results(Q1 but not Q3), click “Search”

58. HKUHKU Computer Centre Using Search Results  After waiting for awhile, SRS give the query result of Query 1 but not Query 3  => Query of all sequences in PIR with description having “cytochrome” string and organism having “pig”, but their super-family having no string of “cytochrome-c”

59. HKUHKU Computer Centre Extended Search: Exercise 15 Minutes Break Please try the following exercises by yourself!

60. HKUHKU Computer Centre Extended Search : Exercise Question 1.  Search all the human DNA sequence entries created after 01-Jan-2003 with sequence length greater than 100000 in EMBL.

61. HKUHKU Computer Centre Extended Search : Exercise Question 1.

62. HKUHKU Computer Centre Extended Search : Exercise Question 1.

63. HKUHKU Computer Centre Extended Search : Exercise Question 1.

64. HKUHKU Computer Centre Extended Search : Exercise Question 1.

65. HKUHKU Computer Centre Extended Search : Exercise Question 1.

66. HKUHKU Computer Centre Extended Search : Exercise Question 2.  Search all the mouse protein sequence entries created before 01-Jul-2002 with NCBI TAX_ID less than 4000 in SWISSPROT.

67. HKUHKU Computer Centre Extended Search : Exercise Question 2.

68. HKUHKU Computer Centre Extended Search : Exercise Question 2.

69. HKUHKU Computer Centre Extended Search : Exercise Question 2.

70. HKUHKU Computer Centre Extended Search : Exercise Question 2.

71. HKUHKU Computer Centre Extended Search : Exercise Question 3.  Using the previous result, search the entries that have links to “PROSITE” database.

72. HKUHKU Computer Centre Extended Search : Exercise Question 3. Identify the Query ID (Q6 in this case, you may not have same query ID)

73. HKUHKU Computer Centre Extended Search : Exercise Question 3. Enter the expression to find the entries in previous that have link to “PROSITE” database (“Q6<PROSITE” in this case, you may not have same query ID)

74. HKUHKU Computer Centre Extended Search : Exercise Question 3. Result similar to this one

75. HKUHKU Computer Centre Introduction to SRS Part 3. Linking related sequence / database

76. HKUHKU Computer Centre Linking Related Sequence first two sequence  Go back to result #3, Click to select the first two sequence Link  Click “ Link ” button to search for the related sequence

77. HKUHKU Computer Centre Linking Related Sequence Find related entries  Ensure the choice “ Find related entries ” EMBL  Click “ EMBL ” as to search related sequence in this databank Search  Click “ Search ” button

78. HKUHKU Computer Centre Linking Related Sequence  Result: 5 entries found in “EMBL” are the the related sequence with your selected sequence

79. HKUHKU Computer Centre Linking Related Sequence  Refine the result list to “SeqSimpleView” in the left panel

80. HKUHKU Computer Centre Linking Related Sequence  Result List

81. HKUHKU Computer Centre Linking database: Exercise 15 Minutes Break Please try the following exercises by yourself!

82. HKUHKU Computer Centre Linking database: Exercise Question 1. Find in the EMBL database the corresponding sequences that link to the longest sequence of the previous result (question #2 in extended search)

83. HKUHKU Computer Centre Linking database : Exercise Question 1. Go back to the previous result Question #2 in extended search(Query #6 in this case)

84. HKUHKU Computer Centre Linking database : Exercise Question 1. Sort to find the longest sequence from the result list

85. HKUHKU Computer Centre Linking database : Exercise Question 1. Sort to find the longest sequence from the result list

86. HKUHKU Computer Centre Linking database : Exercise Question 1. Click the “Link” button after selecting the longest sequence

87. HKUHKU Computer Centre Linking database : Exercise Question 1. Search the “EMBL” database which have related entries links to selected sequence

88. HKUHKU Computer Centre Linking database : Exercise Question 1. EMBL:AP000423 is matched

89. HKUHKU Computer Centre Linking database: Exercise Question 2. Using the previous result (question #1 in simple query), make a query to find the entries which have links to SWISSPROT database

90. HKUHKU Computer Centre Linking database : Exercise Question 2. Go back to the previous result Question #1 in simple query (Query #2 in this case)

91. HKUHKU Computer Centre Linking database : Exercise Question 2. Click the “Link” button with “Unselected only”

92. HKUHKU Computer Centre Linking database : Exercise Question 2. Select “Swissprot”, show only results with related entries link to “Swissprot”

93. HKUHKU Computer Centre Linking database : Exercise Question 2. Around 11 EMBL entries are matched Return list should be EMBL entries but not SWISSPROT entries

94. HKUHKU Computer Centre Linking database: Exercise Question 3. Using the previous result (question #1 in simple query), make a query to find the entries which have no links to SWISSPROT database

95. HKUHKU Computer Centre Linking database : Exercise Question 3. Select “Swissprot”, show only results without related entries

96. HKUHKU Computer Centre Linking database : Exercise Question 3. Around 32 EMBL entries are matched

97. HKUHKU Computer Centre Introduction to SRS Part 4. Application

98. HKUHKU Computer Centre Application: BLAST  Go back to the query result page -> Q9 "(([PIR-ID:ODHU1] | [PIR-ID:ODBO1]) > EMBL )" BLASTN  Click the checkbox of EMBL:MIHSM1 and then click “Launch” with application “ BLASTN ”

99. HKUHKU Computer Centre Application: BLAST Yeast Complete Genome  BLAST window appear and change the “Complete Database to search” to Yeast Complete Genome  Change other parameters as you like and then click “Launch” to execute

100. HKUHKU Computer Centre Application: BLAST  BLAST job was submitted to the batch queue  Click the hourglass icon (left top corner) to check whether the job is finished?

101. HKUHKU Computer Centre Application: BLAST  After the job result is ready, click to see the BLAST job result

102. HKUHKU Computer Centre Application: BLAST  After waiting for awhile, the BLAST result list appear, click any one of them to view the detail

103. HKUHKU Computer Centre Application: BLAST  BLAST alignment result with the databanks

104. HKUHKU Computer Centre Application: Clustalw  Go back to blast result list. Then click the checkbox to select first 5 sequence NClustalW Launch  Click the Application pull down menu to “ NClustalW ” and then click “ Launch ”

105. HKUHKU Computer Centre Application: Clustalw  Then “ClustalW” window appear and change the parameters as you like

106. HKUHKU Computer Centre Application: Clustalw Launch  After click “ Launch ”, SRS would launch clustalw with you selected sequence and give the result

107. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  Using the ClustalW result, and then click “Tools”

108. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  Choose “prettyplotN”, and then click “Launch”

109. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  It jump to “prettyplotN” interface, scroll down …..

110. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  Click to select “Display the consensus”, and then click “Launch”

111. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  Click the first graphic file to view the result, while the second file would be empty

112. HKUHKU Computer Centre Application: EMBOSS(eg: PRETTYPLOT)  You will see the identical residue shown in RED color  The last line show the consensus of the alignment

113. HKUHKU Computer Centre Application: EMBOSS(eg: SIXPACK)  Go back to the query result page -> Q9 "(([PIR-ID:ODHU1] | [PIR-ID:ODBO1]) > EMBL )"  Click the checkbox of EMBL:MIHSM1 and then click “Tools”

114. HKUHKU Computer Centre Application: EMBOSS(eg: SIXPACK)  Choose “ SIXPACK ” and then click “ Launch ”

115. HKUHKU Computer Centre Application: EMBOSS(eg: SIXPACK)  click “ Launch ” to run SIXPACK program

116. HKUHKU Computer Centre Application: EMBOSS(eg: SIXPACK)  At the result page, see the number of possible ORF in 6-frame

117. HKUHKU Computer Centre Application: EMBOSS(eg: SIXPACK)  See the translation in all 6-frames

118. HKUHKU Computer Centre Application: EMBOSS(eg: TMAP)  Several EMBOSS can be directly launched by SRS: for example, TMAP  Go back to Q4 result and click the checkbox of PIR:S26019 and then click “Tools”

119. HKUHKU Computer Centre Application: EMBOSS(eg: TMAP) TMAP  It will jump to show a list of application, change the pull-down menu to “TMAP” and click launch

120. HKUHKU Computer Centre Application: EMBOSS(eg: TMAP)  “TMAP” window appear and click “Launch” to execute TMAP with your selected sequence

121. HKUHKU Computer Centre Application: EMBOSS(eg: TMAP)  After waiting for awhile, “TMAP”give out the predicts transmembrane segments result

122. HKUHKU Computer Centre Application: EMBOSS(eg: TMAP)  Scroll at the bottom to click to see the membrane spanning regions diagram

123. HKUHKU Computer Centre Application : Exercise 15 Minutes Break Please try the following exercises by yourself!

124. HKUHKU Computer Centre Application: Exercise Question 1. Do the sequence alignment of the 5 shortest sequence from the previous result (question #2 in extended search) using clustalw

125. HKUHKU Computer Centre Application: Exercise Question 1. Go back to the previous result Question #2 in extended search, Q6 in this case

126. HKUHKU Computer Centre Application: Exercise Question 1. Sort to find the 5 shortest sequences from the result list

127. HKUHKU Computer Centre Application: Exercise Question 1. Launch “Clustalw” after selecting 5 shortest sequences

128. HKUHKU Computer Centre Application: Exercise Question 1. No need to modify any parameters, click “launch” to start sequence alignment

129. HKUHKU Computer Centre Application: Exercise Question 1.

130. HKUHKU Computer Centre Application: Exercise Question 2. Do the BLAST search using the EMBL:AY278491 (HKU-SARS virus) sequence against EMBL (Release): VRL(virus) database

131. HKUHKU Computer Centre Application: Exercise Question 2. Go back to previous result list(Q2 in normal case) to find the HKU-SARS virus

132. HKUHKU Computer Centre Application: Exercise Question 2. Search against the Viruses database

133. HKUHKU Computer Centre Application: Exercise Question 2. After waiting for few minutes, BLAST result list display

134. HKUHKU Computer Centre Application: Exercise Question 2. See the BLAST result vs TOR2

135. HKUHKU Computer Centre Application: Exercise Question 3. Find the transmembrance segments of the SWISSPROT:VME1_CVHSA (SARS virus M-protein) sequence using TMAP

136. HKUHKU Computer Centre Application: Exercise Question 3. After finding the sequence, launch “tmap”

137. HKUHKU Computer Centre Application: Exercise Question 3. After finding the sequence, launch “tmap”

138. HKUHKU Computer Centre Application: Exercise Question 3.

139. HKUHKU Computer Centre Application: Exercise Question 3.

140. HKUHKU Computer Centre Application: Exercise Question 3.

141. HKUHKU Computer Centre Introduction to SRS Part 5. Others

142. HKUHKU Computer Centre User submit own sequence:  User can submit their own sequence to work with SRS  Go to “Select Databanks”, click to “Expand all” and find the “User Owned Databanks”  Click the “Add Data” beside USERDNA

143. HKUHKU Computer Centre User submit own sequence:  Enter your own DNA sequence in the blank field  Then click “Launch” to input your own sequence to the UserDNA databank

144. HKUHKU Computer Centre User submit own sequence:  Wait for SRS to store your input DNA sequence

145. HKUHKU Computer Centre User submit own sequence:  Your sequence has been successfully input to the USERDNA databank

146. HKUHKU Computer Centre User submit own sequence:  Then you can search related link sequence or launch application with your sequence  For example, you can launch BLAST with your input sequence

147. HKUHKU Computer Centre SRS On-Line Help

148. HKUHKU Computer Centre SRS On-Line Help

149. HKUHKU Computer Centre -END-