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