Preprint available

[Yves Chauvin]

                  **DO NOT FORWARD TO OTHER GROUPS**


The following paper,
"Hidden Markov Models in Molecular Biology: New Algorithms and
Applications",
has been placed in the neuroprose archive.
It is to be published in the Proceedings of the 1992 NIPS conference, 

Further information and retrieval instructions are given below.

Yves Chauvin
yves at netid.com

___________________________________________________________________________


               Hidden Markov Models in Molecular Biology: 
                    New Algorithms and Applications

					         Pierre Baldi 
			           Jet Propulsion Laboratory
			            and Division of Biology, 
			       California Institute of Technology
				           Pasadena, CA 91109

					         Yves Chauvin 
                              Net-ID, Inc.

                            Tim Hunkapiller 
                          Division of Biology 
                  California Institute of Technology 

                          Marcella A. McClure
             Department of Ecology and Evolutionary Biology 
                    University of California, Irvine 


We introduce a new convergent learning algorithm for HMMs that, unlike the
classical Baum-Welch algorithm, is smooth and can be applied on-line or
in batch mode, with or without the usual Viterbi most likely path
approximation.  HMMs are then trained to represent and align several protein 
families including immunoglobulins and kinases.
In all cases, the trained models seem to capture the 
statistical properties characteristic of the families.

___________________________________________________________________________


A complete technical report and related preprints are 
available upon written request to the first author.

___________________________________________________________________________


Retrieval instructions:
The paper is baldi.compbiohmm.ps.Z in the neuroprose archive.

To retrieve this file from the neuroprose archives:

unix> ftp cheops.cis.ohio-state.edu
Name (cheops.cis.ohio-state.edu:becker): anonymous
Password: (use your email address)
ftp> cd pub/neuroprose
ftp> binary
ftp> get baldi.compbiohmm.ps.Z
200 PORT command successful.
150 Opening BINARY mode data connection for baldi.compbiohmm.ps.Z
.
ftp> quit
.
unix> uncompress baldi.compbiohmm.ps.Z
unix> lpr baldi.compbiohmm.ps.Z