Retriving sequences from large local databases

David Mathog mathog at caltech.edu
Wed Mar 16 06:59:21 EST 2005


Rolf wrote:
> I am running local blast on different databases. This works perfectly.
> The problem comes when I want to retrieve sequences from the large
> (and practically not possible to open) databases.
> Can this be done through the BioEdit program?
> Other programs?

I don't know about BioEdit but fastacmd, which is part of the NCBI
toolkit, can do this.

So can the demo program in my blastdb_api package.  You can pick
up the source code for that here:

   ftp://saf.bio.caltech.edu/pub/software/molbio/blastdb_api.tar.gz

Regards,

David Mathog
mathog at caltech.edu
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