profiles from prosite to GCG ??

Stuart M. Brown browns02 at mcrcr.med.nyu.edu
Fri Oct 18 13:25:38 EST 1996

In article <53ia6i$gu0 at rc1.vub.ac.be>, iribhn at ulb.ac.be (iribhn) wrote:

> Hello,
> I'd like to retrieve profile matrixes from Prosite and use them
> in GCG programs (e.g. findpatterns). The only problem is that the
> format are not compatible. Does anybody knows a "translater" that
> can convert a Prosite profile matrix into a GCG profile matrix ?
> Thanks in advance,
> (please email me at cgovaert at ulb.ac.be)
> Cedric Govaerts
> Institut de Recherche Interdisciplinaire
> en Biologie Humaine et Nucleaire
> Universite Libre de Bruxelles
> Brussels Belgium
> cgovaert at ulb.ac.be

I have spent some time playing around with this concept, but in a different way.
Rather than working with the profile matrix, I used the pattern from the
same Prosite entry (I think that the two are roughly eqivalent).  

This pattern needs to be tweaked only a little bit - square brackets to 
curved ones, etc, then it can be used with FINDPATTERNS.  Hoever, I only 
got FINDPATTERNS to accept the new pattern by specifying a text file 
containing it on the command  line, not by typing it in when it asks for 
a pattern interactively.

Hope this helps

Stuart M. Brown, Molecular Biology Consultant 
NYU-MC Research Computing Resource, Dept. of Cell Biology
550 First Ave, New York, NY 10016
Phone: (212)263-7689  FAX: (212)263-8139

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