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

Rong Chen rong at bu.edu
Fri Dec 5 14:40:19 EST 2003

Hi Iddo,

In genomic annotation, we normally create a profiles for each sequence in
the genome, and align these profiles against some databases (such as PDB)
to get annotation. What we found is combine this forward search with a
reverse search helped a lot in detecting remote homologies. The reverse
search means that we create a profile for each sequence in the databases 
(PDB) and align each profile against your genome database. Since depending 
on whether the profile is generated from a query sequence or a template 
sequence, the sequence profile covers different sequence space. Therefore, 
combining direct search with reverse search can increase sensitivity. 
However, when there is only a small number of sequences you want to query, 
we still need to align each profile of PDB against the databases composed 
of your target sequences. If we can combine all profiles of PDB into a 
database, and align your target sequences against this profile databases, 
we can save a lot of computation time. I heard that new Psi-blast has this 
reverse search function, but I could not find it in NCBI's website. Did 
you hear anyting about it?

Thank you.


On Fri, 5 Dec 2003, Iddo Friedberg wrote:

> FFAS does this.
> Was published in:
> L. Rychlewski, L. Jaroszewski, W. Li, A. Godzik (2000), Protein Science 
> 9, 232-241
> (Actually the article refers to an older version of FFAS. The method of 
> the new one is currently in press. But they both do profile-profile 
> alignments).
> You can access the server at:
> http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl
> Cheers,
> Iddo
> Rong Chen wrote:
> > 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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> > 
> > 

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