[Bioperl-l] formatdb with the nr database
smarkel at scitegic.com
Mon Jan 23 17:53:43 EST 2006
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
Hubert Prielinger wrote:
> 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
> Help is very appreciated
> Thank you very much in advance
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: smarkel at scitegic.com
SciTegic Inc. mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253
San Diego, CA 92123 fax: +1 858 279 8804
USA web: http://www.scitegic.com
More information about the Bioperl-l