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I get fewer results with BlastProDom using my local InterProScan installation than when I use EBI InterProScan. Whats wrong?

April 26, 2017EBI fewer installation interproscan local results wrong

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I get fewer results with BlastProDom using my local InterProScan installation than when I use EBI InterProScan. Whats wrong?

1 Answer

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Actually this is not an error. EBI InterProScan uses a larger file from ProDom (prodom.mul available for download from ProDom webiste) which contains all the ProDom entries. Standalone InterProScan uses a smaller file (prodom.ipr) which contains only ProDom entries integrated into InterPro. That explains why on EBI web site appear some entries marked as “unintegrated” which are not in prodom.ipr because they are not integrated into InterPro. Also, if you use a different version of BLAST than the one provided with InterProScan (currently, 2.2.6), you may get different results reported.