[Bioperl-l] All mouse mRNAs

Andrew Walsh walsh at cenix-bioscience.com
Thu Apr 29 11:17:18 EDT 2004

If you know the accession numbers or gis, you could use Batch Entrez 
from the NCBI web site to do a batch download and then use Bio::SeqIO to 
parse the file (whichever format you choose).

If you don't have the accessions handy, you could try parsing them out 
of the Mm.data file from UniGene (look for lines where SEQTYPE=mRNA).


Sean Davis wrote:
> All,
> Sorry to bother with a general question, but I am interested in getting all
> mouse mRNA sequences from genbank.  I only need fasta, but there are
> approximately 300k of these.  Is this even worth attempting via bioperl
> (Bio::DB::Query::Genbank) or is there another way to do this (besides
> locally installing genBank, if I can help it).
> Thanks,
> Sean
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Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Pfotenhauerstr. 108
01307 Dresden, Germany
Tel. +49(351)210-2699
Fax  +49(351)210-1309

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