[Bioperl-l] How to retrieve info about sequence-tagged-sites
Heikki Lehvaslaiho
heikki@ebi.ac.uk
24 Oct 2002 17:49:39 +0100
Alice,
I am afraid there is nothing in BioPerl for accessing UniSTS. We have a
fairly generic set of objects in Bio::Map namespace and a parser for
mapmaker format but nothing more useful.
I know that Hilmar Lapp has been thinking about maps and markers in the
context of BioSQL project so maybe something will happen in near future.
Would you be interested in helping to write something?
I certainly am interested in helping to get somethin going on. The
deCode human map places many old polymorphic markers into sequence for
the first time.
I have not used UniSTS, but it really seems to be resource worth
integrating into BioPerl. One problem is that according the front page
the web interface is Entrez which is quite difficult to work with. Is
there a simpler interface to these data?
The first thing would be to write a parser, Bio::MapIO::unists, that can
handle the format.
-Heikki
P.S. UniSTS home page: http://www.ncbi.nlm.nih.gov/genome/sts
On Thu, 2002-10-24 at 15:16, Alice Lu wrote:
> 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
> _/ _/ _/ Wellcome Trust Genome Campus, Hinxton
> _/ _/ _/ Cambs. CB10 1SD, United Kingdom
> _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>
--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________