Gusfield Dan. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology PDF
Cambridge University Press, 1997. - 556 p.
Traditionally an area of study in computer science, string algorithms have, in recent years, become an increasingly important part of biology, particularly genetics. This volume is a comprehensive look at computer algorithms for string processing. In addition to pure computer science, Gusfield adds extensive discussions on biological problems that are cast as string problems and on methods developed to solve them. This text emphasizes the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics.
Exact String Matching: The Fundamental String Problem
Exact Matching: Fundamental Preprocessing and First Algorithms
Exact Matching: Classical Comparison-Based Methods
Exact Matching: A Deeper Look at Classical Methods
Seminumerical String Matching
Suffix Trees and Their Uses
Introduction to Suffix Trees
Linear-Time Construction of Suffix Trees
First Applications of Suffix Trees
Constant-Time Lowest Common Ancestor Retrieval
More Applications of Suffix Trees
Inexact Matching, Sequence Alignment, Dynamic Programming
The Importance of (Sub)sequence Comparison in Molecular Biology
Core String Edits, Alignments, and Dynamic Programming
Refining Core String Edits and Alignments
Extending the Core Problems
Multiple String Comparison - The Holy Grail
Sequence Databases and Their Uses - The Mother Lode
Currents, Cousins, and Cameos
Maps, Mapping, Sequencing, and Superstrings
Strings and Evolutionary Trees
Three Short Topics
Models of Genome-Level Mutations
Epilogue - where next?
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