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findpatterns

Keith Elliston keith_elliston at merck.com
Wed May 25 15:45:57 EST 1994


> > 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
================================================================================



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