[Bioperl-l] formatdb with the nr database

[Scott Markel]

Hubert,

The .phr et al files are the result of already having run
formatdb.  By running NCBI's fastacmd (comes with blastall
and formatdb) with the -D option, you can get back to a
FASTA file.

Scott

Hubert Prielinger 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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