[Bioperl-l] targetp request
tuco at pasteur.fr
Wed Jan 13 05:24:34 EST 2010
On 1/6/10 7:20 PM, Vijayaraj Nagarajan wrote:
> 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.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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 :
TargetP modules will provides parsed informations about protein
reads in a targetp output file. It parses the results, and
Bio::SeqFeature::Generic object for each sequences found to have
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.
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