[Bioperl-l] refseqs

Sean Davis sdavis2 at mail.nih.gov
Tue Apr 27 16:04:53 EDT 2004

Although this is not a strictly bioperl answer, you can simply use the
genome browser (http://genome.ucsc.edu) table browser to get the exon
sequences for all refseq genes directly.  Go to the refseq positional table,
go to advanced query, choose FASTA as the download type, then you will have
a choice of downloading coding sequence only, UTR's, etc., and other
options.  The exons will each be a separate FASTA sequence with the refseq
ID, chromosome start and end, and other information in the FASTA header
line.  To do all of this takes about 30 seconds.

Hope this helps.

On 4/27/04 3:13 PM, "Phillips, Ken" <kphillips at paragen.com> wrote:

> All - 
> I have a list of refseq mRNA accessions for which I want to parse out
> individual exon sequence for array probe design.  I am not very familiar with
> the bioperl api, and it seems at first glance a rather daunting task as the
> exon coordinates are not present in the refseq flatfile, and not accessible as
> seqFeature objects using the exon tag.  My question is, how does one map
> refseq accessions to coordinates on a genomic contig?
> Any help would be greatly appreciated.
> Thanks,
> KP
> Kenneth L. Phillips
> Bioinformatics Specialist
> Computational Systems Biology
> ParadigmGenetics, Inc.
> 108 T.W. Alexander Drive
> P.O. Box 14528
> Research Triangle Park, NC 27709-4528
> Phone: (919) 425-3000
> Direct: (919) 425-3075
> Cell: (919) 632-9865
> kphillps at paragen.com
> www.paragen.com
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