Book One

Contents

• Prediction

  Shankar Subramaniam, David K. Tcheng, and James M. Fenton

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• Finding Genes in DNA Using Decision Trees and Dynamic Programming

  Steven Salzberg, Xin Chen, John Henderson, and Kenneth Fasman

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• Preface

  David J. States, Pankaj Agarwal, Terry Gaasterland, Lawrence Hunter, and Randall F. Smith

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• Gene Prediction by Pattern Recognition and Homology Search

  Ying Xu and Edward C. Uberbacher

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• HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae

  Peter D. Karp, Christos Ouzounis, and Suzanne Paley

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• Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models

  Anders Gorm Pedersen, Pierre Baldi, Soren Brunak, and Yves Chauvan

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• Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families

  Thomas D. Wu and Douglas L. Brutlag

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• From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination

  Kim Baxter, Evan Steeg, Richard Lathrop, Janice Glasgow, and Suzanne Fortier

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• A Grammar-Based Unification of Several Alignment and Folding Algorithms

  Fabrice Lefebvre

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• GeneFisher–Software Support for the Detection of Postulated Genes

  Robert Giegerich, Folker Meyer, and Chris Schleiermacher

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• A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins

  Paul Horton and Kenta Nakai

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• Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures

  Mark Gerstein and Michael Levitt

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• A Top-Down Approach to Whole Genome Visualization

  K. Heumann, C. Harris, and H. W. Mewes

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• The Megaprior Heuristic for Discovering Protein Sequence Patterns

  Timothy L. Bailey and Michael Gribskov

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• Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing

  Jin Kim, James R. Cole, Eric Torng, and Sakti Pramanik

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• A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA

  David Kulp, David Haussler, Martin G. Reese, and Frank H. Eeckman

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• Genome-Scale DNA Sequence Recognition by Hybridization to Short Oligomers

  Aleksandar Milosavljevic, Suzana Savkovic, Radomir Crkvenjakov, David Salbego, Hope Serrato, Heidi Kreuzer, Anne Gemmell, Shawna Batus, Danica Grujic, Susan Carnahan, and Jovanka Tepavcevic

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• Improving the Quality of Automatic DNA Sequence Assembly Using Fluorescent Trace-Data Classifications

  Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Shavlik, and Frederick R. Blattner

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• The Mathematical Model of Subtractive Hybridization and Its Practical Application

  Olga D. Ermolaeva, Sergy A. Lukyanov, and Eugene D. Sverdlov

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• A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System

  Philipp Bucher and Kay Hofmann

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• Good Maps Are Straight

  Eric Harley, Anthony J. Bonner, and Nathan Goodman

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• Compact Encoding Strategies for DNA Sequence Similarity Search

  David J. States and Pankaj Agarwal

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• Gene Recognition in Cyanobacterium Genomic Sequence Data Using the Hidden Markov Model

  Tetsushi Yada and Makoto Hirosawa

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• Applications of GeneMark in Multispecies Environments

  James D. McIninch, William S. Hayes, and Mark Borodovsky

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• Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation

  Marcella A. McClure, Chris Smith, and Pete Elton

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• Discovering Patterns and Subfamilies in Biosequences

  Alvis Brazma, Inge Jonassen, Esko Ukkonen, and Jaak Vilo

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• Ontological Foundations for Biology Knowledge Models

  Carole D. Hafner and Natalya Fridman

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• Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming

  Burkhard Rost, Rita Casadio, and Piero Fariselli

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