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[go-friends] InterPro -> GO optimization

Mark Wilkinson mark.wilkinson at
Wed Oct 16 01:15:49 PDT 2013

Dear GO Friends,

I have a fairly large number of sequences that I need to run through  
InterProScan.  The primary purpose is to retrieve GO annotations from the  

As you know, some of the algorithms in iprscan are pretty intensive!  I'm  
wondering if anyone has a good feeling for the trade-offs in which iprscan  
programs to run, vs. maximizing the number of GO annotations retrieved.   
Are there some of the programs that are unlikely to return any GO  
matches?  (or more likely to return duplicates from other less  
processor-intensive algorithms?)

Advice appreciated!


Dr. Mark D. Wilkinson
Isaac Peral Senior Researcher, Biological Informatics
Centro de Biotecnología y Genómica de Plantas UPM-INIA (CBGP)
Campus Montegancedo,
Autopista M-40 (Km 38)
28223-Pozuelo de Alarcón (Madrid)

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