[BiO BB] A question about profile database in psi-blast.
dmb at mrc-dunn.cam.ac.uk
Sat Dec 6 08:50:01 EST 2003
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?
++ Iddo Friedberg--
> Slight correction: FFAS aligns a /profile/ against a profile database, not a
> /sequence/ against a profile database. More sensitive that way.
> Rong Chen wrote:
>> 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 Chen, Ph.D.
>> 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
> Iddo Friedberg, Ph.D.
> The Burnham Institute
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037
> Tel: +1 (858) 646 3100 x3516
> Fax: +1 (858) 646 3171
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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