[DI] Re: searching for promoters...

"CatherineLetondal"letondal at pasteur.fr "CatherineLetondal"letondal at pasteur.fr
Thu Jun 1 04:19:29 EST 1995


In article (1995Jun1.065030.6177 at comp.bioz.unibas.ch), "KeithRobison" robison at mito.harvard.edu writes:
>MarkPallen (m.pallen at imperial.ac.uk) wrote:
>: Hi netters
>
>: I should like to search the bacterial section of GenBank for new 
>: potential rpoN promoters. I have come across a consensus for the 
>: promoter sequence in the literature and have used this to do a 
>: FINDPATTERNS search via GCG. However, I doubt that this is the best way 
>: to do things. What I would really like to do is define a consensus where 
>: each position in the consensus is given a score for each residue and 
>: then use to probe the database. Does anyone know of any software or 
>: preferably any WWW site that will allow me to do this kind of search?
>
>You can do this sort of analysis with the profile search programs in
>GCG.  I don't know of a WWW site to do this, but perhaps one will
>show up later this year to do something along these lines...
>
>(though the exact search you describe -- profile versus a large
>database -- is computationally power-hungry).
>

The BIOCCELERATOR at Weizmann Intitute has a Web page for GCG ProfileSearch
and others tools :
http://sgbcd.weizmann.ac.il/Bic/ExecAppl.html

There is also the ISREC Profile Homepage at :
http://ulrec3.unil.ch/profile/profile.html
with informations and references to papers about making profiles from an 
alignment.


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