[Bioperl-l] Retrieve FASTA seqs with NCBI definition line

Mikaela Ilinca Gabrielli MILG at lundbeck.com
Mon Apr 7 14:06:06 EDT 2003


Dear all, 

I'd like to retrieve sequences from GenPept that are in fasta format AND
include the NCBI definition line. I thought this was easy but as I apply
Bio::DB::GenPept I get only a part of the NCBI definition line - missing gi
and accession number information.

ex def-line from NCBI:
>gi|4504379|ref|NP_003658.1| G protein-coupled receptor 49; orphan G
protein-coupled receptor HG38; G protein-coupled receptor 67 [Homo sapiens] 

ex defline retrieved through Bio:

>GPR49 G protein-coupled receptor 49; orphan G protein-coupled receptor
HG38; G protein-coupled receptor 67 [Homo sapiens]

Is there any easy way to get around this or do I have to use
'$seq->primary_id' and '$seq->accession_number' to "cut&paste" my own fasta
records that look like those in NCBI ?

Best regards,

Mikaela



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