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Archive-name: bionet/molbio/prosearch/1991-06-14
Archive: menudo.uh.edu:/pub/genbank-server/unix/prosearch* [129.7.1.6]
Original-posting-by: MACRIDES@wfeb2.bitnet (Foteos Macrides)
Original-subject: Re: PROSITE search program
Reposted-by: emv@msen.com (Edward Vielmetti, MSEN)


>> Hello everybody,
>> I have heard of a program for searching UWGCG-files with
>> the PROSITE database of A. Bairoch.

>I haven't heard of this particular program, but should mention that the EMBL
>netserver has several programs available which facilitate the use of PROSITE
>motifs with the GCG package.  (Some of these may also operate on files in GCG
>format independently, but I'm not sure of the specifics.  In case anyone is
>lacking it, the address of the netserver is Netserv@EMBL-Heidelberg.de.
>
>BTW, v 7 of the GCG package includes a program called Motifs, which searches
>for PROSITE motifs in sequences.  It's fairly intuitive, and produces useful
>output.  I'd recommend using the /Ref qualifier (which prints out brief
>descriptions of all motifs for which hits are found) if you're not already
>familiar with PROSITE.

        We got the p/d program earlier this year via Email from
gene-server@bchs.uh.edu (SEND VMS PROSEARCH12.DCLSHAR).  It requires GAWK
(Free Software Foundation).  We got the VMS port of GAWK by FTP from
RML2.SRI.COM (128.18.22.20).  It also requires READSEQ (I think that's on
NETSERV@EMBL, but we got it from iubio.bio.indiana.edu 129.79.1.101.  Frankly
to my surprise, when we put all these assorted things together the program
worked perfectly.

        We recently installed GCG V7.  MOTIFS is VERY nice.

                                Fote

=========================================================================
 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES@WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545
=========================================================================

-- comp.archives file verification
menudo.uh.edu
-rw-r--r--  1 504      352        214072 Feb 17 21:43 /pub/genbank-server/unix/prosearch_1.2.shar
-rw-r--r--  1 504      352        294983 Feb 17 21:43 /pub/genbank-server/unix/prosearch_1.2.uue
found prosearch ok
menudo.uh.edu:/pub/genbank-server/unix/prosearch*