Book One

Contents

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

  Philipp Bucher and Kay Hofmann

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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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• 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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• 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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• 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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• 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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• Prediction

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

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• The Megaprior Heuristic for Discovering Protein Sequence Patterns

  Timothy L. Bailey and Michael Gribskov

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• A Top-Down Approach to Whole Genome Visualization

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

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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 Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins

  Paul Horton and Kenta Nakai

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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 Grammar-Based Unification of Several Alignment and Folding Algorithms

  Fabrice Lefebvre

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

  Thomas D. Wu and Douglas L. Brutlag

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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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• 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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• Gene Prediction by Pattern Recognition and Homology Search

  Ying Xu and Edward C. Uberbacher

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• Preface

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

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

  Tetsushi Yada and Makoto Hirosawa

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• Compact Encoding Strategies for DNA Sequence Similarity Search

  David J. States and Pankaj Agarwal

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• Good Maps Are Straight

  Eric Harley, Anthony J. Bonner, and Nathan Goodman

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• Applications of GeneMark in Multispecies Environments

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

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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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• Ontological Foundations for Biology Knowledge Models

  Carole D. Hafner and Natalya Fridman

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• Discovering Patterns and Subfamilies in Biosequences

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

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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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