[Bioperl-l] refseqs

Brian Osborne brian_osborne at cognia.com
Tue Apr 27 15:32:16 EDT 2004


The positions of the exons are stored in a SplitLocation object. It sounds
like you could retrieve the mRNAs one-by-one using Bio::DB::RefSeq, find the
"CDS SeqFeature", then use the exon coordinates and the underlying sequence
returned by entire_seq() to get the exons themselves. I'm not sure what you
meant by "genomic contig" though, this approach uses the cDNA sequence. Take
a look at the Feature-Annotation HOWTO
(http://bioperl.org/HOWTOs/html/Feature-Annotation.html) for more

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Phillips, Ken
Sent: Tuesday, April 27, 2004 3:14 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] refseqs

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.

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

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