[Bioperl-l] How to retrieve info about sequence-tagged-sites

[Heikki Lehvaslaiho]

On Wed, 2002-10-23 at 20:19, Alice Lu wrote:
> Hi everyone,
> 
> I have a long list of STS that I like to retrieve the primer information
> for each of them, I have their IDs, is there anyway to use Bioperl to
> retrieve this info automatically? 

You can use Bio::DB::BioFetch/EMBL/GenBank to retrieve the sequences if
you need that. 

What I think you are asking is: Can you design primers for a sequence?

The answer is that bioperl does not have primer design programs built in
but you can access external programs installed locally.
There is a primer3 wrapper Bio::Tools::Primer3 as well as
Bio::Factory::EMBOSS which can access the EMBOSS program primersearch.

The Pise server from Pasteur institute and bioperl modules accessing
programs in there are probably not for you since you work in a company.

Hope this helps,

	-Heikki

 
> Thanks, 
> 
> Alice H. Lu, Ph.D.
> Rubicon Genomics, Inc.
> 4370 Varsity Drive
> Ann Arbor, MI  48108-2241
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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