> > 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>" :-(
>
I got a note from Mike Hogan at GCG, that confirmed this. However, when I looked
at a sample of my search results, I did not find a single sequence of
length>50. When I searched OWL 22 (72,017 sequences) I found 2,320 sequences
that fit the criteria. I also did a couple of searches leaving out the end
constraints.... with the cterm contraint removed, I found 65,845 hits. The
others are still running... :)
I don't know if others have the same results, but it appears that my
findpatterns is working just fine. I am running the vms version, at level 7.3.
Later,
Keith
================================================================================
Keith O. Elliston | Phone: (908)594-6099
Dept. of Bioinformatics | Fax: (908)594-2929
Merck Research Laboratories | Email: Elliston at merck.com
Box 2000 / Mail Stop RY80A-1 | Elliston at aol.com
Rahway, NJ 07065 U.S.A. | Elliston at mbcl.rutgers.edu
================================================================================
