[Bioperl-l] All mouse mRNAs

Hilmar Lapp hlapp at gmx.net
Thu Apr 29 12:16:12 EDT 2004

Do you want all mouse mRNA sequences that were ever submitted to 
GenBank, or do you want mRNAs for all mouse genes?

In the latter case, RefSeq nicely partitions the release by species 
(see the species-specific cumulative updates).

Genbank is partitioned too, so you don't have to parse everything.

At any rate, NCBI will not be thrilled by people downloading 100s of 
thousands of sequences through their query interfaces ...


On Thursday, April 29, 2004, at 07:40  AM, 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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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