Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology
Edited by Terry Gaasterland, Peter Karp, Kevin Karplus, Ghristos Ouzounis, Chris Sander, and Alfonso Valencia
June 21–26, 1997, Halkidiki, Greece. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
Please Note: Abstracts are linked to individual titles, and will appear in a separate browser window. Full-text versions of the papers are linked to the abstract text. Access to full text may be restricted to AAAI members. PDF file sizes may be large!
Contents
Sponsors / vii
Organizing Committee / ix
Preface / xi
Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations / 3
Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Shavlik, and Frederick R. Blattner
Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data / 15
Russ B. Altman, Neil F. Abernethy, and Richard O. Chen
Automatic Annotation for Biological Sequences by Extraction of Keywords from MEDLINE Abstracts: Development of a Prototype System / 25
Miguel A. Andrade and Alfonso Valencia
Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL / 33
Rolf Apweiler, Alain Gateau, Sergio Contrino, Maria Jesus Martin, Vivien Junker, Claire O'Donovan, Fiona Lang, Nicoletta Mitaritonna, Stephanie Kappus, and Amos Bairoch
Self-Organizing Neural Maps of the Coding Sequences of G-Protein-Coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins / 44
P. Arrigo, P. Fariselli, and R. Casadio
Beta-Sheet Prediction Using Inter-Strand Residue Pairs and Refinement with Hopfield Neural Network / 48
Minoru Asogawa
Code Generation through Annotation of Macromolecular Structure Data / 52
John Biggs, Calton Pu, and Philip Bourne
Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison / 56
Ewan Birney and Richard Durbin
Data Mining for Regulatory Elements in Yeast Genome / 65
Alvis Brazma, Jaak Vilo, Esko Ukkonen, and Kimmo Valtonen
Application of Genetic Search in Derivation of Matrix Models of Peptide Binding to MHC Molecules / 75
Vladimir Brusic, Christian Schönbach, Masafumi Takiguchi, Vic Ciesielski, and Leonard C. Harrison
RIBOWEB: Linking Structural Computations to a Knowledge Base of Published Experimental Data / 84
Richard O. Chen, Ramon Feiciano, and Russ B. Altman
Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity / 92
Marie des Jardins, Peter D. Karp, Markus Krummenacker, Thomas J. Lee, and Christos A. Ouzounis
Incorporating Global Information into Secondary Structure Prediction with Hidden Markov Models of Protein Folds / 100
Valentina Di Francesco, Philip McQueen, Jean Garnier, and Peter J. Munson
Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors / 104
Inna Dubchak, Ilya Muchnik, and Sung-Hou Kim
A Knowledge Base for D. melanogaster Gene Interactions Involved in Pattern Formation / 108
Jérôme Euzenat, Christophe Chemla, and Bernard Jacq
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences / 120
Jan Gorodkin, Laurie J. Heyer, and Gary D. Stormo
Domain Identification by Clustering Sequence Alignments / 124
Xiaojun Guan
RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation / 131
Henning Hermjakob, Robert Giegerich, and Walter Arnold
Decision Support System for the Evolutionary Classification of Protein Structures / 140
Liisa Holm and Chris Sander
Better Prediction of Protein Cellular Localization Sites with the k Nearest Neighbors Classifier / 147
Paul Horton and Kenta Nakai
Identifying Chimerism in Proteins Using Hidden Markov Models of Codon Usage / 153
Lawrence Hunter and Barry Zeeberg
The Context-Dependence of Amino Acid Properties / 157
Thomas R. Ioerger
Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method / 167
Ina Koch and Thomas Lengauer
Two Methods for Improving Performance of a HMM and their Application for Gene Finding / 179
Anders Krogh
ANOLEA: A WWW Server to Assess Protein Structures / 187
Francisco Melo, Damien Devos, Eric Depiereux, and Ernest Feytmans
A Fast Heuristic Algorithm for a Probe Mapping Problem / 191
Brendan Mumey
Multi-Body Interactions within the Graph of Protein Structure / 198
Peter J. Munson and Raj K. Singh
Enumerating and Ranking Discrete Motifs / 202
Craig G. Nevill-Manning, Komal S. Sethi, Thomas D. Wu, and Douglas L. Brutlag
Selecting Optimal Oligonucleotide Primers for Multiplex PCR / 210
Pierre Nicodéme and Jean-Marc Steyaert
PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank) / 214
Tamotsu Noguchi, Kentaro Onizuka, Yutaka Akiyama, and Minoru Saito
Automatic Construction of Knowledge Base from Biological Papers / 218
Yoshihiro Ohta, Yasunori Yamamoto, Tomoko Okazaki, Ikuo Uchiyama, and Toshihisa Takagi
Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis / 226
Anders Gorm Pedersen and Henrik Nielsen
Large Scale Protein Modeling and Model Repository / 234
Manuel C. Peitsch
Modeling Antibody Side Chain Conformations Using Heuristic Database Search / 237
David W. Ritchie and Graham J. L. Kemp
Novel Techniques for Visualizing Biological Information / 241
Alan J. Robinson and Tomas P. Flores
A CORBA Server for the Radiation Hybrid Database / 250
P. Rodriguez-Tomé, C. Helgesen, P. Lijnzaad, and K. Jungfer
Extraction of Substructures of Proteins Essential to their Biological Functions by a Data Mining Technique / 254
Kenji Satou, Toshihide Ono, Yoshihisa Yamamura, Emiko Furuichi, Satoru Kuhara, and Toshihisa Takagi
CARTHAGENE: Constructing and Joining Maximum Likelihood Genetic Maps / 258
Thomas Schiex and Christine Gaspin
Modeling Transcription Factor Binding Sites with Gibbs Sampling and Minimum Description Length Encoding / 268
Jonathan Schug and G. Christian Overton
Adding Semantics to Genome Databases: Towards an Ontology for Molecular Biology / 272
Steffen Schulze-Kremer
Predicting Enzyme Function from Sequence: A Systematic Appraisal / 276
Imran Shah and Lawrence Hunter
Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations / 284
Amit P. Singh and Douglas L. Brutlag
The Gene-Finder Computer Tools for Analysis of Human and Model Organisms Genome Sequences / 294
Victor Solovyev and Asaf Salamov
Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions / 303
Jens Stoye, Dirk Evers, and Folker Meyer
Protein Model Representation and Construction / 307
M. Sullivan, J. Glasgow, E. Steeg, L. Leherte, and S. Fortier
Automated Alignment of RNA Sequences to Pseudoknotted Structures / 311
Jack E. Tabaska and Gary D. Stormo
Inference of Molecular Phylogenetic Tree Based on Minimum Model-Based Complexity Method / 319
Hiroshi Tanaka, F. Ren, T. Okayama, and T. Gojobori
A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser / 329
Yutaka Ueno and Kiyoshi Asai
SEALS: A System for Easy Analysis of Lots of Sequences / 333
D. Roland Walker and Eugene V. Koonin
Better Cutters for Protein Mass Fingerprinting: Preliminary Findings / 340
Michael J. Wise, Tim Littlejohn, and Ian Humphery-Smith
Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags / 344
Ying Xu, Richard J. Mural, and Edward C. Uberbacher
Functional Prediction of B. subtilis Genes from Their Regulatory Sequences / 354
Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, and Kenta Nakai
Bayesian Adaptive Alignment and Inference / 358
Jun Zhu, Jun Liu, and Charles Lawrence
Index / 369