>On 14 Jun 91 00:26:00 GMT,
>MACRIDES at wfeb2.bitnet (Foteos Macrides) said:
>> We got the p/d program earlier this year via Email from
>>gene-server at 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 at 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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