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[go-friends] InterPro -> GO optimization

mitchell at ebi.ac.uk mitchell at ebi.ac.uk
Thu Oct 17 04:17:54 PDT 2013


Hi Mark,
That's an interesting question. I am pretty sure that there is no
correlation between
efficiency/speed of InterProScan analyses and the quality/coverage of GO
terms.
Some of the InterProScan analyses that offer high sequence coverage can
return less
information-rich GO terms, but they are actually fairly quick to run.

Have you tried using the latest version of InterProScan (version 5)? It
has an inbuilt
sequence look up service that might speed the processing up. You can
download it
from here: http://code.google.com/p/interproscan/wiki/Introduction
If all else fails, you could send us your sequences and we'd be happy to
run the analysis
and return the GO terms to you.

I hope this helps.
Alex

Dr A L Mitchell
InterPro team


> 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
> IPR2Go.
>
> 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!
>
> Mark
>
>
>
> --
> 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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>



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