profile searching

Sean Eddy eddy at wol.wustl.edu
Fri Jul 21 10:59:51 EST 1995

   > I'm looking for a public domain profile searching prog, akin to the GCG
   > profilesearch prog. Does anybody know if this exists, as I can't
   > find anything like it in any of the software repositories.

Two hidden Markov model (HMM) software packages for protein and
nucleic acid searches are freely available (though not public domain).
HMMs are a formal instantiation of sequence profiles. Neither package
can read profiles directly, but HMMs can be built from multiple
alignments just as profiles can.

	home page for HMMER, source and documentation for
	my HMM software package

	home page for SAM, source and documentation for
	the HMM package from David Haussler and colleagues    
	at UC Santa Cruz

- Sean Eddy
- Dept. of Genetics, Washington University School of Medicine
- eddy at genetics.wustl.edu

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