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

[Martin Gollery]

Rong,

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!

Marty


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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 


Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042


-------------------------------------------------
This mail sent through https://webmail.unr.edu