KHOFMANN@cipvax.biolan.Uni-Koeln.DE (Kay Hofmann) (06/13/91)
Hello everybody,
I have heard of a program for searching UWGCG-files with
the PROSITE database of A. Bairoch.
The program was called PROSITE (or the like) and was written
by Clemens Broger from Ciba Geigy.
Does anybody know, if this program is publicly available or can
anybody supply me with the e-mail address of the author? The address
i got seems not to be functional.
thank you,
Kay
------------------------------------------------------------------------
Kay Oliver Hofmann Tel. ++49 201 478 6980
Institut fuer Biochemie (med. Fak.) FAX ++49 201 478 6979
Universitaet Koeln
Joseph Stelzmann Str. 52 INTERNET:
D-5000 Koeln 41 KHOFMANN@cipvax.biolan.uni-koeln.de
------------------------------------------------------------------------bailey@hmivax.humgen.upenn.edu (06/14/91)
In article <1991Jun13.142700.122934@rrz.uni-koeln.de>, KHOFMANN@cipvax.biolan.Uni-Koeln.DE (Kay Hofmann) writes: > 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. Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Human Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@hmivax.humgen.upenn.edu (IN 128.91.200.37) !-------------------------------------------------------------------------------
MACRIDES@wfeb2.bitnet (Foteos Macrides) (06/14/91)
>> 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 =========================================================================
MACRIDES@wfeb2.bitnet (Foteos Macrides) (06/14/91)
>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 ========================================================================= Foteos Macrides Worcester Foundation for Experimental Biology MACRIDES@WFEB2.BITNET 222 Maple Avenue, Shrewsbury, MA 01545 =========================================================================