[Bioperl-l] Hello

[michael watson (IAH-C)]

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.

Simples.
________________________________________
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

Hi,
One of these should get you most of the way to what you need.
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_using_a_query.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_the_DNA_sequence_using_EntrezGene_IDs.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

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


Hope this helps,

Russell

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?

--
Regards,
Chirag Matkar,
BTech Bioinformatics,
Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,
http://www.dypbbi.edu.in
Pune.

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