[BiO BB] A question about profile database in psi-blast.

Martin Gollery mgollery at unr.edu
Fri Dec 5 14:42:39 EST 2003


This is called RPS-BLAST. You can run this locally, or use it on the NCBI 
website. They have a database called CDD that is a great combination of Pfam, 
Smart and COG. The psi-blast format is pretty good, considering the speed that 
you get out of it!


Quoting Rong Chen <rong at bu.edu>:

> Hi,
> Normally, we align a profile against a sequence database in psi-blast. I
> heard that we could also cat all profiles to create a database, and align
> a sequence against this profile database. Did anyone hear anything about
> it? Is it a new program or a new option in psi-blast?
> Thank you.
> Rong
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Rong Chen, Ph.D.
> Scientist
> Protein Engineering
> Accelrys Inc.
> San Diego, CA 92121
> Tel: (858)799-5304(office)
> E-mail: rong at zlab.bu.edu   http://zlab.bu.edu/~rong
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> _______________________________________________
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330

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