Help:How can I retrieve Interpro domains for a given species

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You can retrieve the InterPro data using the BioMart tool: 

       http://biomart.vectorbase.org/biomart/martview/


E.g. with the Anopheles gambiae:

  • Go on the BioMArt page,
  • Choose the VectorBase (Ensembl 48) database and the Anopheles gambiae (AgamP3.4) dataset,
  • Click on the Attributes link (left menu bar) and select the following from the Protein section:
    • InterPro Description
    • InterPro ID
  • Then click on the Filters link (left menu bar) and select the following from the Protein section:
    • Limit to genes with these family of domain IDs
  • and toggle the menu to 'with InterPro IDs'

That's the query done, this will ask for a list of peptides which have associated InterPro domains (the filter part) and will return a table containing the GeneID, TranscriptID, InterPro Acc, InterPro description (the attribute part). You can download the file in a number of formats.

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