Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology
Edited by Janice Glasgow, Tim Littlejohn, François Major, Richard Lathrop, David Sankoff, and Christoph Sensen
June 28–July 1, 1998, Montréal, Québec, Canada. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
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Contents
ISMB Organization / vii
ISMB Sponsors / viii
Preface / ix
The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection / 2
Pankaj Agarwal and Vineet Bafna
Compression of Strings with Approximate Repeats / 8
L. Allison, T. Edgoose, and T. I. Dix
Calculating the Exact Probability of Language-Like Patterns in Biomolecular Sequences / 17
Kevin Atteson
TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources / 25
Patricia G. Baker, Andy Brass, Sean Bechhofer, Carole Goble, Norman Paton, and Robert Stevens
Computational Applications of DNA Structural Scales / 35
Pierre Baldi, Søren Brunak, Yves Chauvin, and Anders Gorm Pedersen
Advanced Query Mechanisms for Biological Databases / 43
I-Min A. Chen, Anthony S. Kosky, Victor M. Markowitz, Ernest Szeto, and Thodoros Topaloglou
A Statistical Theory of Sequence Alignment with Gaps / 52
Dirk Drasdo, Terence Hwa, and Michael Lässig
IMGT/LIGM-DB: A Systematized Approach for ImMunoGeneTics Database Coherence and Data Distribution Improvement / 59
Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc
The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories / 69
Nathan Goodman, Steve Rozen, and Lincoln D. Stein
Hierarchical Minimization with Distance and Angle Constraints / 78
John R. Gunn
BioSim--A New Qualitative Simulation Environment for Molecular Biology / 85
Karsten R. Heidtke and Steffen Schulze-Kremer
GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome / 95
N. A. Kolchanov, M. P. Ponomarenko, A. E. Kel, Yu. V. Kondrakhin, A. S. Frolov, F. A. Kolpakov, T. N. Goryachkovsky, O. V. Kel, E. A. Ananko, E. V. Ignatieva, O. A. Podkolodnaya, V. N. Babenko, I. L. Stepanenko, A. G. Romashchenko, T. I. Merkulova, D. G. Vorobiev, S. V. Lavryushev, Yu. V. Ponomarenko, A. V. Kochetov, G. B. Kolesov, V. V. Solovyev, L. Milanesi, N. L. Podkolodny, E. Wingender, and T. Heinemeyer.
Modeling Protein Homopolymeric Repeats: Possible Polyglutamine Structural Motifs for Huntington’s Disease / 105
Richard H. Lathrop, Malcolm Casale, Douglas J. Tobias, J. Lawrence Marsh, and Leslie M. Thompson
Segment-Based Scores for Pairwise and Multiple Sequence Alignments / 115
Burkhard Morgenstern, William R. Atchley, Klaus Hahn, and Andreas Dress
Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model / 122
Henrik Nielsen and Anders Krogh
Bayesian Protein Family Classifier / 131
Kunbin Qu, Lee Ann McCue, and Charles E. Lawrence
Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis / 140
Eric C. Rouchka and David J. States
A Surface Measure for Probabilistic Structural Computations / 148
Jeanette P. Schmidt, Cheng C. Chen, Jonathan L. Cooper, and Russ B. Altman
Identification of Divergent Functions in Homologous Proteins by Induction over Conserved Modules / 157
Imran Shah and Lawrence Hunter
Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains / 165
Kimmen Sjölander
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences / 175
Erik L. L. Sonnhammer, Gunnar von Heijne, and Anders Krogh
A Computational System for Modeling Flexible Protein-Protein and Protein-DNA Docking / 183
Michael J. E. Sternberg, Patrick Aloy, Henry A. Gabb, Richard M. Jackson, Giden Moont, Enrique Querol, and Francesc X. Aviles
Genetic Algorithms for Protein Threading / 193
Jacqueline Yadgari, Amihood Amir, and Ron Unger
Automated Clustering and Assembly of Large EST Collections / 203
David P. Yee and Darrell Conklin
A Map of the Protein Space–An Automatic Hierarchical Classification of all Protein Sequences / 212
Golan Yona, Nathan Linial, Naftali Tishby, and Michal Linial
Index / 222
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