[DI] Re: searching for promoters...

"SteveThompson"stevet at deoxy.vadms.wsu.edu "SteveThompson"stevet at deoxy.vadms.wsu.edu
Thu Jun 1 16:27:44 EST 1995

In Article (1995Jun1.065030.6177 at comp.bioz.unibas.ch), "Keith Robison"
robison at mito.harvard.edu wrote:
>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).

Another GCG solution, less cpu intensive, are the two programs Consensus and
FitConsensus.  These deal only with nucleic acid sequences and use much
simpler algorithms than the profile suite.  Refer to the GCG help
documentation for details.  I have reformatted GCG Consensus style weight
matrix descriptions of several eukaryote regulatory domains including
Bucher's TATA, Cap, CCAAT, and GC_box, and McLauchlan's terminator
consensus.  Contact me if you would like these data files.

                                                        - Steve

                                Steven M. Thompson
              Consultant in Molecular Genetics and Sequence Analysis
        Visualization, Analysis & Design in the Molecular Sciences (VADMS)
             Washington State University, Pullman, WA 99164-1224, USA
            AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                     INTERnet:  THOMPSON at jaguar.csc.wsu.edu

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