Pattern matching software

Nathan Siemers nathan at rna.wi.mit.edu
Wed Mar 11 08:09:17 EST 1998


Tim Bailey's MEME and MAST programs now have the ability to look for
protein motifs in nucleotide databases.  Not exactly findpattern type
searches, but perhaps could be used as such.


http://www.sdsc.edu/MEME


nathan




tjrc1 at mole.bio.cam.ac.uk (Tim Cutts) writes:
> 
> I am looking for some UNIX pattern matching software, similar to GCG's
> findpatterns, but which will allow me to compare a protein pattern against a
> nucleotide sequence database translated on the fly in all six reading
> frames.  Does such a program exist?  If not I am willing to try writing
> one, although I can't believe no-one has already done this...
> 
> Thanks in advance.
> 
> Tim.
> 

-- 
Nathan Siemers, Ph.D. 
Research Investigator, Applied Genomics
Bristol-Myers Squibb Pharmaceutical Research Institute
Visiting Scientist
Whitehead/MIT Center for Genome Research
617-252-1382 
siemers at bms.com





More information about the Bio-soft mailing list