Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology
Edited by Russ Altman, Douglas Brutlag, Peter Karp, Richard Lathrop, and David Searls
August 14–17, 1994, Stanford, California. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
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Contents
Sponsors / ix
Program Committee / x
Preface / xi
Russ Altman, Douglas Brutlag, Peter Karp, Richard Lathrop, and David Searls
The Repeat Pattern Toolkit (RPT): Analyzing the Structure and Evolution of the C. elegans Genome / 1
Pankaj Agarwal and David J. States
Constraint Satisfaction Techniques for Modeling Large Complexes: Application to the Central Domain of 16S Ribosomal RNA / 10
Russ B. Altman, Bryn Weiser, and Harry F. Noller
Finding an Average Core Structure: Application to the Globins / 19
Russ B. Altman and Mark Gerstein
Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer / 28
Timothy L. Bailey and Charles Elkan
An Intelligent System for Comparing Protein Structures / 37
Ethan Benatan
Protein Design by Optimization of a Sequence-Structure Quality Function / 44
Steven E. Brenner and Alan Berry
A Generalized Profile Syntax for Biomolecular Sequence Motifs and Its Function in Automatic Sequence Interpretation / 53
Philipp Bucher and Amos Bairoch
Integration of Competing Ancillary Assertions in Genome Assembly / 62
Christian Burks, Rebecca J. Parsons, and Michael L. Engle
Design and Application of a C++ Macromolecular Class Library / 70
Weider Chang, Ilya N. Shindyalov, Calton Pu, and Philip E. Bourne
Genetic Map Construction with Constraints / 78
Dominic A. Clark, Christopher J. Rawlings, and Sylvie Doursenot
VQLM: A Visual Query Language for Macromolecular Structural Databases / 87
Dawn Cohen, Kumar Vadaparty, Bill Dickinson and Hemanth Salem
Knowledge Discovery of Multilevel Protein Motifs / 96
Darrell Conklin, Suzanne Fortier, and Janice Glasgow
Using Interval Logic for Order Assembly / 103
Zhan Cui
A Restriction Mapping Engine Using Constraint Logic Programming / 112
Trevor I. Dix and Chut N. Yee
Stochastic Motif Extraction Using Hidden Markov Model / 121
Yukiko Fujiwara, Minoru Asogawa, and Akihiko Konagaya
Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs / 130
Terry Gaasterland, Natalia Maltsev, Jorge Logo, and Guo-Hua Chen
RNA Modeling Using Gibbs Sampling and Stochastic Context Free Grammars / 138
Leslie Grate, Mark Herbster, Richard Hughey, David Haussler, I. Saira Mian,
and Harry Noller
Creating a Knowledge Base of Biological Research Papers / 147
Carole D. Hafner, Kenneth Baclawski, Robert P. Futrelle, Natalya Fridman,
and Shobana Sampath
The Prediction of the Degree of Exposure to Solvent of Amino Acid Residues Via Genetic Programming / 156
Simon Handley
A Flexible Approach to Genome Map Assembly / 161
Eric Harley and Anthony J. Bonner
Prototyping a Genetics Deductive Database / 170
Catherine Hearne, Zhan Cui, Simon Parsons, and Saki Hajnal
Induction of Rules for Biological Macromolecular Crystallization / 179
Daniel Hennessy, Vanathi Gopalakrishnan, Bruce G. Buchanan, John M.
Rosenberg, and Devika Subramanian
Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites / 188
John M. Heumann, Alan S. Lapedes, and Gary D. Stormo
Aligning Genomes with Inversions and Swaps / 195
J. L. Holloway and P. Cull
Representations of Metabolic Knowledge: Pathways / 203
Peter D. Karp and Suzanne M. Paley
An Efficient Method for Multiple Sequence Alignment / 212
Jin Kim and Sakti Pramanik
Inductive Logic Programming Used to Discover Topological Constraints in Protein Structures / 219
Ross D. King, Dominic A. Clark, Jack Shirazi, and Michael J. E.
Sternberg
Toward Unification of Taxonomy Databases in a Distributed Environment / 227
Hajime Kitakami, Yoshio Tateno, and Takashi Gojobori
Discovering Side-Chain Correlations In [[alpha]]-Helices / 236
Tod M. Klinger and Douglas L. Brutlag
Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming / 244
John R. Koza
DNA Sequence Analysis Using Hierarchical ART-based Classification Network / 253s
Cathie LeBlanc, Charles R. Katholi, Thomas R. Unnasch, and Susan I. Hruska
Segmentation and Interpretation of 3D Protein Images / 261
Laurence Leherte, Kim Baxter, Janice Glasgow, and Suzanne Fortier
High Speed Pattern Matching in Genetic Data Base with Reconfigurable Hardware / 269
Eric Lemoine, Joel Quinqueton and Jean Sallantin
Predicting Location and Structure Of [[beta]]-Sheet Regions Using Stochastic Tree Grammars / 276
Hiroshi Mamitsuka and Naoki Abe
Kinematic Manipulation of Molecular Chains Subject to Rigid Constraints / 285
Dinesh Manocha and Yunsha Zhu
Describing Multiple Levels of Abstraction in the Metabolism / 294
Michael L. Mavrovouniotis
Sequence Comparisons via Algorithmic Mutual Information / 303
Aleksandar Milosavljevic
Flow Cytometry Data Analysis: Comparing Large Multivariate Data Sets Using Classification Trees / 310
Joseph Norman
The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein / 314
Kentaro Onizuka, Masayuki Akahosi, Masato Ishikawa, and Kiyoshi Asai
Geometric Problems in Molecular Biology and Robotics / 322
David Parsons and John Canny
Intelligent DNA-Based Molecular Diagnostics Using Linked Genetic Markers / 331
Dhiraj K. Pathak, Eric P. Hoffman, and Mark W. Perlin
Distributed Machine Learning: Scaling Up with Coarse-grained Parallelism / 340
Foster John Provost and Daniel N. Hennessy
GeneQuiz: A Workbench for Sequence Analysis / 348
Michael Scharf, Reinheard Schneider, Georg Casari, Peer Bork, Alfonso
Valencia, Christos Ouzounis, and Chris Sander
The Prediction of Human Exons By Oligonucleotide Composition and Disriminant Analysis of Spliceable Open Reading Frames / 354
Victor V. Solovyev, Asaf A. Salamov, and Charles B. Lawrence
An Expert System for Processing Sequence Homology Data / 363
Erik L. L. Sonnhammer and Richard Durbin
Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence / 369
Gary D. Stormo and David Haussler
An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequence / 376
Yin Xu, J. Ralph Einstein, Richard J. Mural, Manesh Shah, and Edward C.
Uberbacher