[Bioperl-l] formatdb with the nr database

Tim Erwin taerwin at gmail.com
Mon Jan 23 18:21:03 EST 2006


The .phr, .pnd, .pin, .pni, .ppd files are the indexed database, you
don't need to run formatdb as this step has already been done. If you
run formatdb on a fasta file it will generate these .p* files for a
protein database and .n* files for a nucleotide database.

 Regards,

 Tim

On 1/24/06, Hubert Prielinger <hubert.prielinger at gmx.at> wrote:
> Hi,
> I have downloaded the nr database for doing a blast search locally, now
> I'm supposed to index the database with formatdb, but it doesn't work...
> The online help says that you need a fasta file that is indexed to use
> for searching the database, but when I uncompressed the zip file, there
> were only .phr, .pnd, .pin, .pni, .ppd file....
> Is there anybody who can tell me, how to use formatdb with the nr
> database...
>
> Help is very appreciated
> Thank you very much in advance
>
> Hubert
>
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