This section aims to familiarise users with using InterProScan as a tool to annotate and characterize sequences.

Follow the procedure outlined below to analyse the sequences:

  1. Click to open an InterProScan window
  2. Click on one of the sequence files provided.
  3. Cut and paste the sequence into the sequence search form,select the applications to run, select a reading frame size, select 'interactive run' and submit
  4. The result is returned either as the 'Picture View' directly to your browser
  5. Using the tool bar buttons look at the various output formats: Table View, Raw Output, and XML output
  6. Mouse-over the matching methods; a pop-up windows appears that provides the boundaries of the method, its match status, the E-value of the match and the name of the method
  7. From the Picture View identify what the InterPro entries represent: FAMILIES, DOMAINS, REPEATS etc
  8. Utilising the links identify which provides a link to the SRS or InterPro view of the entry and note the differences
  9. Are there any PARENT/CHILD or CONTAINS/FOUND IN relationships associated with the returned InterPro entries?
  10. In the SRS view of the Interpro entry click on the PARENT/CHILD red/blue triangles to see the related entries
  11. In the InterPro view click on PARENT/CHILD 'tree' to view the family tree of the entry
  12. Use the InterPro view of the InterPro entry to identify the taxonomic range of the protein FAMILY or DOMAIN. If the entry contains a SMART or Pfam signature go their home pages and compare the taxonomy information to the InterPro taxonomy view
  13. Are there any Gene Ontology terms linked to the InterPro entries? If so, view the terms in QuickGO using the link from the entries
  14. Use the GO ID in the text search to list all InterPro entries associated with this GO term. Also search for the term in QuickGO, the view of the term will show any InterPro entries linked to the term
  15. From the InterProScan results in SRS, link to the appropriate GO terms by choosing 'Link', then ticking GO and 'Submit link'. This is another way of retrieving the associated GO terms and all other InterPro entries these terms are associated with
  16. Use BLAST to identify the sequence with the best homology. Does the BLAST result support the InterProScan result?

  18. Finally, what annotation would you apply to the protein sequence given the InterProScan and BLAST results?

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