[Bioperl-l] targetp request
Kevin Brown
Kevin.M.Brown at asu.edu
Wed Jan 13 18:01:42 UTC 2010
Sounds like this module might be in the wrong place then. Sounds more
like a SeqIO or AlignIO module, heheh. Also looks like the docs might
need to be cleaned up a bit for english readability (at least that
initial sentence).
Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Emmanuel Quevillon
> Sent: Wednesday, January 13, 2010 3:25 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] targetp request
>
> 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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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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