[Bioperl-l] GO terms not present in Swiss annotation object

Chris Fields cjfields at uiuc.edu
Tue Nov 21 01:19:59 EST 2006


The DBLink objects should be generated.  You'll need to give us a bit  
more information to go on, though.  We need an example sequence, your  
local version of Bioperl, maybe a test script, etc.

This is the right forum for this, yes, if you are using BioPerl.


On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote:

> Hi,
>   I'm writing a simple application to extract various fields from  
> swissprot objects and I can't access the GO terms found in  
> "dblink" part of the swiss format flat files.  I'm not a  
> professional programmer and I can't figure out why this is  
> occuring.  All the other "dblink" keys are being  
> generated as far as I can tell (e.g. embl, pfam, etc).  The GO  
> terms are just skipped over and it's driving me crazy.  Not sure if  
> this is a bug or a deliberate strategy I'm unfamiliar with.  I  
> apologize if this is not the correct forum to ask for this sort of  
> help and would ask to be directed to the proper one.
> Juan Cristobal Vera
> Graduate Student
> Department of Biology
> Penn State University
> 208 Mueller Laboratory
> University Park, PA 16802
> (814)863-2957
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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