Algorithms on strings, trees, and sequences: computer science and computational biology

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Algorithms on Strings, Trees, and Sequences Title Page Contents Preface Part I Exact String Matching: The Fundamental String Problem 1 Exact Matching: Fundamental Preprocessing and First Algorithms 2 Exact Matching: Classical Comparison-Based Methods 3 Exact Matching: A Deeper Look at Classical Methods 4 Seminumerical String Matching Part II Suffix Trees and Their Uses 5 Introduction to Suffix Trees 6 Linear-Time Construction of Suffix Trees 7 First Applications of Suffix Trees 8 Constant-Time Lowest Common Ancestor Retrieval 9 More Applications of Suffix Trees Part III Inexact Matching, Sequence Alignment, Dynamic Programming 10 The Importance of (Sub)sequence Comparison in Molecular Biology 11 Core String Edits, Alignments, and Dynamic Programming 12 Refining Core String Edits and Alignments 13 Extending the Core Problems 14 Multiple String Comparison - The Holy Grail 15 Sequence Databases and Their Uses - The Mother Lode Part IV Currents, Cousins, and Cameos 16 Maps, Mapping, Sequencing, and Superstrings 17 Strings and Evolutionary Trees 18 Three Short Topics 19 Models of Genome-Level Mutations Epilogue - Where Next? Bibliography Glossary Index