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[go-friends] InterPro -> GO optimization

Mark markw at illuminae.com
Thu Oct 17 05:52:40 PDT 2013


> 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.


OK, no worries.  I just wondered if there were some that could be  
completely excluded w.r.t the likelihood of getting some GO anotation from  
it.


> 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.


Yup, that's the one I am planning to run.


> 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.


Thank you for the offer!  I'm fine - there's no problem with running the  
analyses, I just wanted to eliminate anything that wasn't going to be  
"productive".  My trial runs so far have me calculating about 28-30 days  
of InterProScanning :-)  That's fine, though!

Cheers!

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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