[Bioperl-l] targetp request

Kevin Brown Kevin.M.Brown at asu.edu
Wed Jan 13 13:01:42 EST 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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