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Date:         Thu, 12 Nov 1992 16:08:54 -0500
Reply-To:     "(Mark A. Gunnell)" <GUNNELL@FCRFV2.NCIFCRF.GOV>
              <INFO-GCG@UTORONTO.BITNET>
From:         "(Mark A. Gunnell)" <GUNNELL@FCRFV2.NCIFCRF.GOV>
Subject:      Re: FindPatterns question
Comments: To: INFO-GCG%UTORONTO.BITNET@fcs280s.ncifcrf.gov,
              agoodrid@VAXA.WEEG.UIOWA.EDU

Stephen Klautky (AGOODRID@VAXA.WEEG.UIOWA.EDU) writes:

> I am using GCG 7.1 on a VAX.  I would like to do searches
> with certain combinations of patterns but I am not sure
> how to set it up.

> For example I want to search a sequence with the following
> pattern:  Motif1(N){0,6}Motif2

> Motifs 1 and 2 are a set of short sequences; right now there
> are 20, each 6 bp.  I want to search *all* combinations of
> this list of motifs.

> To bring biology into this - Motifs 1 and 2 are half-site
> binding sequences for transcription factors.

> In the past I simply used FIND to locate all half sites for a
> given sequence then by hand waded through the spacing requirements.
> This is usually not a problem.  But when you add mismatches then
> things get really messy because if a motif is 5-6 bp you get a long
> list.  Whereas with 2 or 3 mismatches using Motif1(N){0,6}Motif2
> that problem is minimized.
>
> Any hints or comments are appreciated.

> -=] Stephen Klautky [=-    AGOODRID@VAXA.WEEG.UIOWA.EDU
> Biochemistry Dept., University of Iowa, Iowa City, IA. 52242

Stephen -

   I have placed a copy of PatternGen in our anonymous ftp account on
ncifcrf.gov in the /pub/patterngen subdirectory.  I think that this program
should accomplish the task you outlined above.  If not, let me know and I
may be able to modify the program to suit your requirements, or you may
wish to modify the program yourself.

   PatternGen is designed to accept two files of motifs.  One file contains
a list of motifs that will precede a fixed or invariant motif (ie. your
"(N){0,6}" above) and the second file contains  a list of motifs that
follow the invariant.  These could be the same file.  PatternGen then
generates a GCG FindPatterns compatible Pattern.Dat file which combines the
information from the two files and the invariant motif in all combinations.

   PatternGen is written in VAX/VMS Pascal; if you do not have access to a
VAX Pascal compiler, a copy of the executable is included in that directory.
To transfer the programs and example files via  anonymous ftp, do the
following:

   $ ftp ncifcrf.gov
   Username: anonymous
   Password: your_email_address
   NCIFCRF.GOV> cd /pub/patterngen
   <CWD command successful.
   NCIFCRF.GOV> mget *
   NCIFCRF.GOV> bin
   NCIFCRF.GOV> get patterngen.exe
   NCIFCRF.GOV> quit
   $ Purge patterngen.exe


If you place the Patterngen.exe file in your Sys$Login directory,
and define the program as a foreign command:

   $ PatternGen:==$Sys$login:PatternGen.exe

you can then use the program as follows:

   $ PatternGen PreMotif.dat PostMotif.dat Pattern.dat (N){0,6}

Output is in the Pattern.dat file.  To use this data file in conjunction with
the GCG FindPatterns program:

   $ FindPatterns/Data=Pattern.dat

If you have any problems with the program or any unanswered questions,
please let me know.

-Mark
-------------------------------------------------------------------------------
Mark A. Gunnell                   | Internet: gunnell@ncifcrf.gov
Sci. Applications Analyst         | Bitnet:   gunnell%ncifcrf.gov@cunyvm.bitnet
Biomedical Supercomputer Center   | Phone:   (301) 846-5779
PRI/DynCorp                       |
NCI-FCRDC                         |
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Frederick, MD 21702-1201  USA     |
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