[Bioperl-l] Hello

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Sun Feb 14 14:51:15 EST 2010

If I was going to do this, I wouldn't use BioPerl.

I'd download the RefSeq entry for the genome (Mtb)
Then I would use the EMBOSS extractfeat program to extract fasta sequences of the gene features.

From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell [Russell.Smithies at agresearch.co.nz]
Sent: 14 February 2010 19:43
To: 'chirag matkar'
Cc: 'bioperl-l at lists.open-bio.org'
Subject: Re: [Bioperl-l] Hello

One of these should get you most of the way to what you need.

You may find it easier if you have the gene id numbers rather than just the gene names.

Hope this helps,


From: chirag matkar [mailto:chirag.matkar at gmail.com]
Sent: Saturday, 13 February 2010 11:16 p.m.
To: Smithies, Russell
Subject: Hello

Hello Sir,
i am working on Bioperl and have a doubt.
I have aList of gene names of Mtb H37Rv and i want to retrieve FASTA format of all sequences
How can i do that?

Chirag Matkar,
BTech Bioinformatics,
Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,

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