ISMB99 Tutorial Material

Making the most of your hidden Markov models
Handout Material

This tutorial is intended for people who know what an HMM is but want to know how to use them most effectively. It details the tricks used in the SAM-T98 method (in 1998 the best method for remote homology detection in proteins). One feature of this tutorial is the use of sequence logos on a running example to show how various operations change what is being searched for.

• Presentation material
  • Presentation transparencies, one per page.
  • Presentation transparencies, four per page.
  • T98-query.mail
    Sample web results from querying the 2crd protein sequence against a structure database.
  • build-target98-alignment.mail
    Sample web results from building a SAM-T98 alignment for 2crd.
• Introductory material on hidden Markov models
  • ``Profile hidden Markov models'' Sean R. Eddy, Bioinformatics 14(9):755-63, 1998.
  • ``Hidden Markov Models and Protein Sequence Analysis'' Rachel Karchin, UCSC.
• Performance of hidden Markov models
  • ``Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods'' Jong Park, Kevin Karplus, Christian Barrett, Richard Hughey, David Haussler, Tim Hubbard, and Cyrus Chothia, JMB 284(4):1201-1210, 1998
  • ``hidden Markov models for detecting remote protein homologies'' Kevin Karplus, Christian Barrett, and Richard Hughey, Bioinformatics 14(10):846-856, 1998
  • ``Predicting protein structure using only sequence information'', by Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, and Richard Hughey, Proteins: Structure, Function, and Genetics (to appear in 1999).
• Null models, regularizers, and other accessory material
  • ``Scoring hidden Marov models'' Christian Barrett, Richard Hughey, and Kevin Karplus, CABIOS, 13(2):191-199, 1997.
  • ``Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology'' Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, and David Haussler, CABIOS, 12(4):327-345, August 1996.
  • ``Evaluating regularizers for estimating distributions of amino acids'' Kevin Karplus, In ISMB-95, Menlo Park, CA, July 1995. AAAI/MIT Press.
• Other Material
  • SAM-T98 perl script

This document was generated using the LaTeX2HTML translator Version 97.1 (release) (July 13th, 1997) Copyright © 1993, 1994, 1995, 1996, 1997, Nikos Drakos, Computer Based Learning Unit, University of Leeds. Last modified: Wednesday July 21 1999