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Introduction to SRS

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

  2. Introduction to SRS Part 0. Introduction

  3. SRS Introduction • SRS system started out as aSequence Retrieval Systemthat employed sophisticatedparsing and indexingof database text files

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

  5. Starting SRS • Browse the BIOSUPPORT Hompage: http://bioinfo.hku.hk/ • Select “Tools” Option

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

  7. SRS Main Page • After successful login, the default page is a “Temporary Project”.

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

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

  10. 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. Permanent Project • All the query and job result will be saved in your “Permanent Project”.

  12. Permanent Project Option • “Save to desktop” : download & save your project info to your local machine

  13. Permanent Project Option • “Rename project” : change the name of your project

  14. Permanent Project Option • “Delete project” : delete all the related information of your current project

  15. “Quick Searches” page : • Quick access with default databank selection

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

  17. “Quick Text Search” • Default Databank Setting:

  18. Introduction to SRS Part 1. Simple Query

  19. Simple query • Go back to “Select Databank”, click on “PIR” to select “PIR” databank

  20. Simple query • Then click the “Query” button to fill in the query form

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

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

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

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

  25. Gene Sequence • SRS would display the PIR:S26019 description: including ID, accession number, description, keywords, etc

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

  27. Gene Sequence • Scroll down to see the gene function and the gene sequence

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

  29. Gene Sequence • Click the “Output to” button to choose the text/html format

  30. Gene Sequence • Click the “Use View” button to choose the “Complete entries” format

  31. Gene Sequence • Then click “save” to save again the PIR:S26019 to your local machine

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

  33. Simple query: Exercise Question 1. • Search all the “SARS virus” in EMBL databases

  34. Simple query: Exercise • 1. Search all the “SARS virus” in EMBL databases

  35. Simple query: Exercise • 1. Search all the “SARS virus” in EMBL databases

  36. Simple query: Exercise • 1. Search all the “SARS virus” in EMBL databases:

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

  38. Simple query: Exercise • 2. Click to see the detail AY278488

  39. Simple query: Exercise • 2. Click to see the detail AY278488

  40. Simple query: Exercise • 2. Count the number of CDS entries

  41. 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. Simple query: Exercise Question 3. • What is the protein ID for EMBL:AY278741 (SARS coronavirus Urbani) spike glycoprotein?

  43. Simple query: Exercise • 3. Click to see the detail AY278741

  44. Simple query: Exercise • 3. EMBL:AY278741

  45. Simple query: Exercise • 3. EMBL:AY278741

  46. 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. Simple query: Exercise • 4. EMBL:AY278741

  48. Simple query: Exercise • 4. Find biological function of VGL2_CVHSA

  49. Simple query: Exercise • 4. Find biological function of VGL2_CVHSA

  50. Introduction to SRS Part 2. Extended Search