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From: MACRIDES@wfeb2.bitnet (Foteos Macrides)
Newsgroups: bionet.software
Subject: Re: PROSITE search program
Message-ID: <9106141423.AA09212@genbank.bio.net>
Date: 14 Jun 91 15:23:00 GMT
Article-I.D.: genbank.9106141423.AA09212
Sender: daemon@genbank.bio.net
Distribution: bionet
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>On 14 Jun 91 00:26:00 GMT,
>MACRIDES@wfeb2.bitnet (Foteos Macrides) said:
>>         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.
>
>Thanks for the positive advertisement.
>
>I work the ProSearch program. It does require a bit more effort than I
>like for VMS but on unix awk is considered as always present.
>
>Does GCG's motif do more that prosearch?
>
>Frank Kolakowski

        MOTIFS includes the definitions and how the hits met them in the
report, e.g.:

Lipocalin           (D,E,N,S,T)x{3,4}(L,I,V,F,Y)xGxW(F,Y,W,R,H)x(L,I,V,M)
                                    (D)x{3}(L)xGxW(Y)x(I)
             2:     Q                   DFAELQGKWYTI                    VIAAD

This is more informative than PROSEARCH's report of hits simply as positions
(and the PROSITE #'s and motif name), e.g.:

PS00213        2->14    LIPOCALIN               PDOC00187

Otherwise, they're essetially the same.

        I should have mentioned explicitly that PROSEARCH has the equivalent
of MOTIFS's /ref qualifier (option to fetch and include the relevant abstracts
in the report).  Also, the IUBio Archive changed its name this week to
ftp.bio.indiana.edu.

        I should also have mentioned in my "positive advertisement" that if
one does go to the trouble of getting and installing GAWK on a VMS system,
PROSEARCH is an EXCELLENT model for doing useful things with a variety of
p/d databases.

                                Fote

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