[Bioperl-l] formatdb with the nr database

[Tim Erwin]

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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