1 / 149

Introduction to SRS

Introduction to SRS. Frankie Cheung frankie@cc.hku.hk. Introduction to SRS. Part 0. Introduction. SRS Introduction. SRS system started out as a Sequence Retrieval System that employed sophisticated parsing and indexing of database text files. SRS Introduction.

zhen
Download Presentation

Introduction to SRS

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related