From: Othmar Pfannes <wopf at chbs.CIBA.COM>
Newsgroups: bionet.software.gcg
Subject: searching profiles in PROSITE
Date: 27 Apr 1995 16:21:53 +0100
Message-ID: <3nocqh$oev at mserv1.dl.ac.uk>
Dear Netters,
I would appreciate any help re the following problem :
The PROSITE database seems to contain 2 kinds of "Motif" entries:
a) patterns like ....ABCDEFG..
b) profiles in terms of matrices
It seems like I can use the GCG program "motifs" to identify
patterns within PROSITE that are contained in my sequence.
But "motifs" seems to neglect PROSITE info presented as matrices.
Correct?
If yes, then which GCG program allows me to identify motifs that are
represented as matrices within PROSITE?
If there is none, are there other programs available?
Remark:
It seems like that the GCG program "profilescan" does not do the job .
It only checks a
"validated" profile data file that also contains info like gap penalties
and parameters for normalizing scores and which is not included in
PROSITE.
Thanks for your help
Othmar
--
====================================================================
|| ||
Dr. Othmar Pfannes || ||
CIBA || Vox: + 41 + 61 + 697 8685 ||
IS/Scientific Services || ||
R-1008.Z2.22 || Fax: + 41 + 61 + 697 8973 ||
CH-4002 Basel || ||
Switzerland || Internet: wopf at chbs.CIBA.COM ||
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>>>
--
====================================================================
|| ||
Dr. Othmar Pfannes || ||
CIBA || Vox: + 41 + 61 + 697 8685 ||
IS/Scientific Services || ||
R-1008.Z2.22 || Fax: + 41 + 61 + 697 8973 ||
CH-4002 Basel || ||
Switzerland || Internet: wopf at chbs.CIBA.COM ||
|| ||
=====================================================================
