[Bioperl-l] All mouse mRNAs

Sean Davis sdavis2 at mail.nih.gov
Thu Apr 29 13:42:00 EDT 2004

Hilmar and others,

Thanks to everyone who replied.  I was interested in essentially dbEST
entries for mouse which is available as a single file via FTP from ncbi in
the dbest directories (at least the FASTA).  It looks like the file is
compiled and updated on a relatively regular basis and contains all ESTs for
mouse contained in genBank.  There is an analogous file for human, if anyone
is in need of such a thing.


On 4/29/04 12:16 PM, "Hilmar Lapp" <hlapp at gmx.net> wrote:

> 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 ...
> -hilmar
> 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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