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

[Iddo Friedberg]

I think that Martin's answer covers that.



Rong Chen wrote:
> 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.
> 
> Rong
> 
> 
> 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
>>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>
>>>_______________________________________________
>>>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
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>>>
>>>
>>
>>
> 
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-- 
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