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valines

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Tue May 24 04:47:59 EST 1994


In <chhall-230594170308 at chhall.monsanto.com> chhall at bb1t.monsanto.com writes:

> 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.

I realized a similar problem some weeks ago with nucleotide sequences. The
"<" and ">" constraints didn't work either on "<X{1,49}X>" :-(

Regards
  Christoph Gartmann


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