[Bioperl-l] targetp request

Emmanuel Quevillon tuco at pasteur.fr
Wed Jan 13 05:24:34 EST 2010


On 1/6/10 7:20 PM, Vijayaraj Nagarajan wrote:
> Hi,
>
> I am trying to use targetP in bioperl.
> the documentation at the bioperl site is a bit confusing to me...
>
> I would appreciate if you could give a very small example, as to how to use
> "Bio::Tools::TargetP" to predict the localization of a protein sequence that
> i have stored as a string.
>
> Thanks,
> Vijay
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Dear Vivay,

Bio::Tools::TargetP is not intended to run targetp on a sequence but to 
read and parse results from targetp run.

 From the Pod doc :

DESCRIPTION
        TargetP modules will provides parsed informations about protein 
localization.  It
        reads in a targetp output file.  It parses the results, and 
returns a
        Bio::SeqFeature::Generic object for each sequences found to have 
a subcellular
        localization


So to analyze your sequence, you'll first need to run targetp on your 
sequence file to create a targetp result output file. Then use 
Bio::Tools::TargetP module to parse this result file and get only 
informations you want/need from the result to be display as shown in the 
SYNOPSIS of the Pod documentation of the module.

HTH

Regards

Emmanuel


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