The profiles (MATRIX-entries) in Prosite are written in a format
that is an extension of the profile-format used in present versions
of the GCG programs. This new format contains much more informations
than the old one, allowing
- an increased sensitivity in profile searches, and
- the storage of prosite-related informations, scaling options,
probability calculations and options how to handle multiple matches
in a single sequence.
Together with the next release of PROSITE, we (that is Philipp Bucher
and myself) will release a set of programs that can be used for
sequence/profile comparisons and database searches.
At the moment there are only two profiles in Prosite, these are mainly
intended as demonstration items and for testing the programs that are
under development. With the next release of PROSITE, the number of Profiles
will increase to about 10-20, all these profiles are manually optimized
and offer a very high sensitivity in finding the respecive motifs/domains.
We will also provide a WWW-server for doing profile searches by then.
I hope that the addition of profiles will prove to be a valuable extension
ISREC Bioinformatics Group
Swiss Insitute for Experimental Cancer Research
1066 Epalinges s/Lausanne