Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparision

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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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Table of Contents

Ch. 1 An Overview of Sequence Comparison 1
Pt. I Macromolecular Sequences 45
Ch. 2 Recognition of Patterns in Genetic Sequences 55
Ch. 3 Fast Algorithms to Determine RNA Secondary Structures Containing Multiple Loops 93
Pt. II Time-warping, Continuous Functions, and Speech Processing 121
Ch. 4 The Symmetric Time-Warping Problem: From Continuous to Discrete 125
Ch. 5 Use of Dynamic Programming in a Syllable-Based Continuous Speech Recognition System 163
Ch. 6 Application of Sequence Comparison to the Study of Bird Songs 189
Pt. III Variations on a Theme: Algorithms for Related Problems 211
Ch. 7 On the Complexity of the Extended String-to-String Correction Problem 215
Ch. 8 An Analysis of the General Tree-Editing Problem 237
Ch. 9 Simultaneous Comparison of Three or More Sequences Related by a Tree 253
Ch. 10 An Anthology of Algorithms and Concepts for Sequence Comparison 265
Ch. 11 Dissimilarity Measures for Clustering Strings 311
Pt. IV Computational Complexity 323
Ch. 12 Recent Results on the Complexity of Common-Subsequence Problems 325
Ch. 13 Formal-Language Error Correction 331
Ch. 14 How to Compute String-Edit Distances Quickly 337
Pt. V Random Sequences 351
Ch. 15 An Upper-Bound Technique for Lengths of Common Subsequences 353
Ch. 16 Probabilistic Behavior of Longest-Common-Subsequence Length 359
Ch. 17 Common Subsequences and Monotone Subsequences 363
Author Index 367
Subject Index 371
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