[Bioperl-l] Refseq Ids

[Stephen Baird]

Perhaps a Ensembl person could answer....
Is every REFSEQ ID for a genome mapped onto the genomic sequence in
ENSEMBL.
...and is every REFSEQ ID for a genome mapped to an Ensembl gene?

Stephen

On Mon, 20 Sep 2004, Jason Stajich wrote:

>
> On Sep 20, 2004, at 5:21 AM, Marques Bonet wrote:
>
> > Thanks for your suggestions, but it's quite strange that there isn't
> > any method to obtain a simple list of all refSeq Id's of a genome.
> >
> >  But, it is possible to obtain a complete list of all genes with
> > another nomenclature (Locus ID, Accession number, etc...)?
>
> Try EnsMart: http://www.ensembl.org
>
> >
> > Thanks.
> > >From: "Sean Davis" <sdavis2 at mail.nih.gov>
> >  >To: "Jeremy Semeiks" <jrs at farviolet.com>,        "Tomas Marques"
> > <tomas_marques at hotmail.com>,        <bioperl-l at portal.open-bio.org>
> >  >Subject: Re: [Bioperl-l] Refseq Ids
> >  >Date: Sun, 19 Sep 2004 19:38:28 -0400
> >  >
> >  >I haven't checked rat directly, but I think they are also available
> > at the
> >  >same place as genbank flat files, in case you need that detail.
> >  >
> >  >
> >  >----- Original Message -----
> >  >From: "Jeremy Semeiks" <jrs at farviolet.com>
> >  >To: "Tomas Marques" <tomas_marques at hotmail.com>;
> >  ><bioperl-l at portal.open-bio.org>
> >  >Sent: Sunday, September 19, 2004 5:07 PM
> >  >Subject: Re: [Bioperl-l] Refseq Ids
> >  >
> >  >
> >  > > On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote:
> >  > > > How can I obtain all RefSeq IDs from Rat genome? (using
> > BioPerl, of
> >  > > > course...)
> >  > > >
> >  > > >
> >  > > >
> >  > > > I'm using Bio::DB::RefSeq but I have not been able to locate any
> >  > > > method(inherit or not)to do it...
> >  > >
> >  > > Hi Tomas,
> >  > >
> >  > > The most straightforward way to do this might be to download the
> > rat
> >  > > Refseq files directly. They're at
> >  > >
> >  > > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/
> >  > >
> >  > > You should be able to use the Bioperl FASTA parser (part of the
> > SeqIO
> >  > > module) to parse these.
> >  > >
> >  > > HTH,
> >  > > Jeremy
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> >  >
> >  >
> >
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> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
>
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