Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
Edited by David J. States, Pankaj Agarwal, Terry Gaasterland, Lawrence Hunter, and Randall F. Smith
June 12–15, 1996, St. Louis, Missouri. Published by The AAAI Press, Menlo Park, California
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Contents
Program Committee / ix
Preface / xi
David J. States, Pankaj Agarwal, Terry Gaasterland, Lawrence Hunter, and Randall F. Smith
Improving the Quality of Automatic DNA Sequence Assembly Using
Fluorescent Trace-Data Classifications / 3
Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Shavlik, and Frederick R. Blattner
The Megaprior Heuristic for Discovering Protein Sequence Patterns / 15
Timothy L. Bailey and Michael Gribskov
From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination / 25
Kim Baxter, Evan Steeg, Richard Lathrop, Janice Glasgow, and Suzanne Fortier
Discovering Patterns and Subfamilies in Biosequences / 34
Alvis Brazma, Inge Jonassen, Esko Ukkonen, and Jaak Vilo
A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System / 44
Philipp Bucher and Kay Hofmann
The Mathematical Model of Subtractive Hybridization and Its Practical Application / 52
Olga D. Ermolaeva, Sergy A. Lukyanov, and Eugene D. Sverdlov
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures / 59
Mark Gerstein and Michael Levitt
GeneFisher--Software Support for the Detection of Postulated Genes / 68
Robert Giegerich, Folker Meyer, and Chris Schleiermacher
Ontological Foundations for Biology Knowledge Models / 78
Carole D. Hafner and Natalya Fridman
Good Maps Are Straight / 88
Eric Harley, Anthony J. Bonner, and Nathan Goodman
A Top-Down Approach to Whole Genome Visualization / 98
K. Heumann, C. Harris, and H. W. Mewes
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins / 109
Paul Horton and Kenta Nakai
HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae / 116
Peter D. Karp, Christos Ouzounis, and Suzanne Paley
Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing / 125
Jin Kim, James R. Cole, Eric Torng, and Sakti Pramanik
A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA / 134
David Kulp, David Haussler, Martin G. Reese, and Frank H. Eeckman
A Grammar-Based Unification of Several Alignment and Folding Algorithms / 143
Fabrice Lefebvre
Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation / 155
Marcella A. McClure, Chris Smith, and Pete Elton
Applications of GeneMark in Multispecies Environments / 165
James D. McIninch, William S. Hayes, and Mark Borodovsky
Genome-Scale DNA Sequence Recognition by Hybridization to Short Oligomers / 176
Aleksandar Milosavljevic, Suzana Savkovic, Radomir Crkvenjakov, David Salbego, Hope Serrato, Heidi Kreuzer, Anne Gemmell, Shawna Batus, Danica Grujic, Susan Carnahan, and Jovanka Tepavcevic
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models / 182
Anders Gorm Pedersen, Pierre Baldi, Soren Brunak, and Yves Chauvan
Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming / 192
Burkhard Rost, Rita Casadio, and Piero Fariselli
Finding Genes in DNA Using Decision Trees and Dynamic Programming / 201
Steven Salzberg, Xin Chen, John Henderson, and Kenneth Fasman
Compact Encoding Strategies for DNA Sequence Similarity Search / 211
David J. States and Pankaj Agarwal
Prediction / 218
Shankar Subramaniam, David K. Tcheng, and James M. Fenton
Discovering Empirically Conserved Amino Acid Substitution Groups in
Databases of Protein Families / 230
Thomas D. Wu and Douglas L. Brutlag
Gene Prediction by Pattern Recognition and Homology Search / 241
Ying Xu and Edward C. Uberbacher
Gene Recognition in Cyanobacterium Genomic Sequence Data Using the Hidden Markov Model / 252
Tetsushi Yada and Makoto Hirosawa
Index / 261