[Bioperl-l] formatdb with the nr database

Scott Markel 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
FASTA file.


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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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 mailing list