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

[Martin Gollery]

Yes, it is. The reason is that searching with individual sequences relys on 
standard generic scoring matrices, which are based on substitution rates over 
an entire dataset. There is no information on importance of location in a PAM 
or Blosum matrix, which is a serious flaw- some locations in a protein cannot 
be substituted without changing the function of the protein. Other positions 
are not critical at all. Smith-Waterman, Fasta and BLASt searches do not know 
anything about position, and so do not consider this information.

Marty

Quoting Dan Bolser <dmb at mrc-dunn.cam.ac.uk>:

> 
> Is a profile better at detecting homologues than each of its individual
> sequences?
> 
> Is the whole more than the sum of its parts?
> 
> This is generally the impression people have of profiles, but is it true?
> 
> Cheers.
> Dan.
> 
> ++ Iddo Friedberg--
> > Slight correction: FFAS aligns a /profile/ against a profile database,  not
> a
> > /sequence/ against a profile database. More sensitive that way.
> >
> > ./I
> >
> >
> > 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
> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>
> >>
> >> _______________________________________________
> >> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >>
> >>
> >
> > --
> > Iddo Friedberg, Ph.D.
> > The Burnham Institute
> > 10901 N. Torrey Pines Rd.
> > La Jolla, CA 92037
> > USA
> > Tel: +1 (858) 646 3100 x3516
> > Fax: +1 (858) 646 3171
> > http://ffas.ljcrf.edu/~iddo
> >
> > _______________________________________________
> > BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> 
> 
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> 


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


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