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
