[Bioperl-l] Accesssing local database

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Thu Aug 31 05:28:58 EDT 2006


Kamesh,

Not a bioperl solution, but if your sequences are also available from
GenBank (as opposed to your local DB) this is very easy using the 'Batch
Entrez' tool on the NCBI site:

http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Protein

Just upload your list of accession numbers...

Derek.

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of kamesh
narasimhan
Sent: 30 August 2006 17:19
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Accesssing local database

Hi,

I am new to programming world....and now i have this daunting task at
hand.....

I have a text file in which there is a list of accession numbers one in
each
line. I would like to know as to how I can go about retrieving the
sequences, that correspond to these set of accession numbers from a
local
protein database (fasta format) . Which bioperl module (currently
available)
is suited for this??......or do I have to write my own modules....

thanks a lot....
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