Conrad Halling chhall at bb1t.monsanto.com
Wed May 25 11:32:08 EST 1994

In article <chhall-230594170308 at chhall.monsanto.com>, 
     chhall at bb1t.monsanto.com (Conrad Halling) wrote:

> In article <199405232028.NAA29657 at net.bio.net>,
>      keith_elliston at merck.com (Keith Elliston) wrote:
> > Actually, using the GCG package on the vax, you can use findpatterns to  
> > answer the question.  Use the pattern <~V{1,49}~V> to search your favorite 
> > database. (ie., N-term not val, followed by 1-49 residues that are not val,  
> > and the cterm)
> > If you want to use the sequences for some other analyses, or as a database,
> > use the /names option.
> This is an approach that completely escaped me.  This approach is far
> superior since it is more flexible -- you don't have to write a new program
> every time you change your search criteria.  Unfortunately, I cannot find a
> way to limit the search to proteins of fewer than 50 residues in length
> since the "<" and ">" constraints don't seem to work as advertised.  I can
> limit the overhead somewhat by using the command line qualifier
> "/exclude=50,20000", but the results still include sequences of 50 or more
> residues.

For anyone else following this discussion, the original participants
received an e-mail from Michael Hogan at GCG who said that a bug in version
7.x of FindPatterns prevents the successful use of both "<" and ">".  This
has been fixed in the forthcoming version 8.0.
Conrad Halling
Computational Molecular Biologist
Monsanto Co., St. Louis
chhall at bb1t.monsanto.com

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