[Bioperl-l] SeqIO-based parser for Vector NTI sequence files

Cook, Malcolm MEC at stowers.org
Mon Feb 9 09:50:46 EST 2009


What do you expect to extract from the COMMENT lines?

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Scott Markel
Sent: Tuesday, October 21, 2008 3:49 PM
To: bioperl-ml
Cc: smarkel at accelrys.com
Subject: [Bioperl-l] SeqIO-based parser for Vector NTI sequence files

I'm looking for a BioPerl-related solution to parsing Vector NTI sequence files.  The genbank.pm parser will work, but it doesn't parse the COMMENT lines beyond grabbing the simple string value, so it misses all of the added information in those lines.

If you know of any existing code, I'd be interesting in hearing about it.  I checked BioPerl, BioJava, and EMBOSS documentation.
I also checked the Invitrogen web site.


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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