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Get Species Information From Interopro Domain

Hi All,

I was wondering if it would be possible to fetch the list of organism where the domain of interest is present (input will be interpro id). Does any one know how to do this.

RT.

domain
• 3,178 views • link
updated by sarahhunter sarahhunter • written by GR GR

1 answer

You can use the InterPro BioMart to get this information - and because BioMart has built in APIs, you can do it programmatically too.

Here's how:

  1. Go to the InterPro BioMart
  2. From the "CHOOSE DATABASE" drop down menu, select "InterPro BioMart"
  3. From the "CHOOSE DATASET" drop down, select "Protein Matches"
  4. Click on "Filters" in the Left Hand menu, then expand the "InterPro Match Filters" section in the Right Hand panel, by clicking on the [+] icon
  5. Enter the InterPro accession(s) that you are interested in in the "InterPro Entry Accession" list box
  6. Click on "Attributes" in the Left Hand menu and check the check boxes for "InterPro Entry ID", NCBI Taxonomy ID, Taxonomy Name (Species)
  7. Click on "Results" button in the top menu
  8. Check the "Unique results only" check box and choose how you want to view the data

I made a canned query for IPR000001 (Kringle) here: http://www.ebi.ac.uk/interpro/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=protein.default.protein_attributes.entry_ac|protein.default.protein_attributes.taxonomy_scientific_name|protein.default.protein_attributes.protein_tax_id&FILTERS=protein.default.protein_filterpage.entry_ac.'IPR000001'&VISIBLEPANEL=resultspanel

• 5 views • link
written by sarahhunter sarahhunter

Great. Thanks a lot.

• 1 views • link
written by GR GR

I hope you voted for this answer and you should also mark it as accepted if it works for you.

• 1 views • link
written by Neilfws Neilfws

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