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

[Alice Lu]

Hi Heikki,

My apology--I should have explained in more detail. 

The STS are stored in uniSTS database on NCBI website, have IDs like
stSG44393, etc. after searching, the NCBI website displays its primer
sequences and other related info. I guess my question would be if
Bioperl have some thing to search a STS based on its ID and then parse
this web interface to retrieve the primer information. 

Thanks, 

Alice H. Lu, Ph.D.
Rubicon Genomics, Inc.
4370 Varsity Drive
Ann Arbor, MI  48108-2241
Direct Dial Phone No. (734) 677-6893
Email: alicelu@rubicongenomics.com 
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-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk] 
Sent: Wednesday, October 23, 2002 5:17 PM
To: Alice Lu
Cc: bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] How to retrieve info about
sequence-tagged-sites

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
> ____________________________________________
>  
> This message may contain confidential and/or privileged information.
If
> you are not the addressee or authorized to receive this for the
> addressee, you must not use, copy, disclose or take any action based
on
> this message or any information herein.  If you have received this
> message in error, please advise the sender immediately by reply e-mail
> and delete this message.  Thank you for your cooperation. 
> ____________________________________________
>  
>  
> 
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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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