Time Warps, String Edits, and Macromolecules

The Theory and Practice of Sequence Comparision

By: David Sankoff, Joseph Kruskal

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Paperback | 28 January 2000 | Edition Number 1

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Time Warps, String Edits and Macromolecules is a young classic in computational science. The computational perspective is that of sequence processing, in particular the problem of recognizing related sequences. The book is the first, and still best compilation of papers explaining how to measure distance between sequences, and how to compute that measure effectively. This is called string distance, Levenshtein distance, or edit distance. The book contains lucid explanations of the basic techniques; well-annotated examples of applications; mathematical analysis of its computational (algorithmic) complexity; and extensive discussion of the variants needed for weighted measures, timed sequences (songs), applications to continuous data, comparison of multiple sequences and extensions to tree-structures. This theory finds applications in molecular biology, speech recognition, analysis of bird song and error correcting in computer software.

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Non-Fiction Mathematics Probability & Statistics Computing & I.T.Computer Science Science Physics Business Applications Mathematical & Statistical Software Calculus & Mathematical Analysis Business & Management Information Technology General Issue

Ethical & Social Aspects of IT

An Overview of Sequence Comparison	p. 1
Macromolecular Sequences	p. 45
Recognition of Patterns in Genetic Sequences	p. 55
Fast Algorithms to Determine RNA Secondary Structures Containing Multiple Loops	p. 93
Time-warping, Continuous Functions, and Speech Processing	p. 121
The Symmetric Time-Warping Problem: From Continuous to Discrete	p. 125
Use of Dynamic Programming in a Syllable-Based Continuous Speech Recognition System	p. 163
Application of Sequence Comparison to the Study of Bird Songs	p. 189
Variations on a Theme: Algorithms for Related Problems	p. 211
On the Complexity of the Extended String-to-String Correction Problem	p. 215
An Analysis of the General Tree-Editing Problem	p. 237
Simultaneous Comparison of Three or More Sequences Related by a Tree	p. 253
An Anthology of Algorithms and Concepts for Sequence Comparison	p. 265
Dissimilarity Measures for Clustering Strings	p. 311
Computational Complexity	p. 323
Recent Results on the Complexity of Common-Subsequence Problems	p. 325
Formal-Language Error Correction	p. 331
How to Compute String-Edit Distances Quickly	p. 337
Random Sequences	p. 351
An Upper-Bound Technique for Lengths of Common Subsequences	p. 353
Probabilistic Behavior of Longest-Common-Subsequence Length	p. 359
Common Subsequences and Monotone Subsequences	p. 363
Author Index	p. 367
Subject Index	p. 371
Table of Contents provided by Blackwell. All Rights Reserved.

Time Warps, String Edits, and Macromolecules

The Theory and Practice of Sequence Comparision

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