Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology

by Dan Gusfield

Overview

String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises 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. Its discussion of current algorithms and techniques also makes it a reference for professionals.

Product Details

ISBN-13:	9781139636285
Publisher:	Cambridge University Press
Publication date:	05/28/1997
Sold by:	Barnes & Noble
Format:	eBook
File size:	10 MB

About the Author

Daniel M. Gusfield, Ph.D., UC Berkeley, 1980. Professor Gusfield's primary interests involve the efficiency of algorithms, particularly for problems in combinatorial optimization and graph theory. These algorithms have been applied to study data and computer security, stable matching, network flow, matroid optimization, and string/pattern matching problems. Currently, Professor Gusfield is focused on string and combinatorial problems that arise in computational biology and bioinformatics.

Table of Contents

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. Semi-numerical 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 and 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 database and their uses: the motherlode; 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.

Editorial Reviews

"...an important summary of the state of the art in pattern matching and an indicator of the importance biological problems have assumed among many researchers. It will hopefully encourage them to question the importance of the problems they endeavor to solve." SIGACT News

"The book will be profitable both for graduate students in computer science and for biologists with a good background in programming." Mathematical Reviews

"One often encounters in this book thought-provoking quotes relating to the importance of sequence analysis...Also found in the text are interesting biological examples of sequence analysis..." Cell

From the Publisher