Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences [Hardcover]

Gonzalo Navarro (Author), Mathieu Raffinot (Author)

Book Description

ISBN-10: 0521813077 | ISBN-13: 978-0521813075 | Publication Date: May 27, 2002 | Edition: 1

Recent years have witnessed a dramatic increase of interest in sophisticated string matching problems, especially in information retrieval and computational biology. This book presents a practical approach to string matching problems, focusing on the algorithms and implementations that perform best in practice. It covers searching for simple, multiple and extended strings, as well as regular expressions, and exact and approximate searching. It includes all the most significant new developments in complex pattern searching. The clear explanations, step-by-step examples, algorithm pseudocode, and implementation efficiency maps will enable researchers, professionals and students in bioinformatics, computer science, and software engineering to choose the most appropriate algorithms for their applications.

Editorial Reviews

Review

"This book is on the domain of searching.... [It] is actually unique on the subject." Mathematical Reviews

Book Description

Recent years have witnessed a dramatic increase of interest in sophisticated string matching problems, mainly arising from information retrieval and computational biology. In this book, the authors present several new string matching algorithms, developed to handle these complex new problems. Unlike most other books, the emphasis is those techniques that work best in practice, which are also the simplest ones in general. The clear explanations, step-by-step examples, algorithm pseudocode, and implementation efficiency maps will enable researchers, professionals and students in bioinformatics, computer science, and software engineering to choose the most appropriate algorithms for their applications.

Product Details

• Hardcover: 232 pages
• Publisher: Cambridge University Press; 1 edition (May 27, 2002)
• Language: English
• ISBN-10: 0521813077
• ISBN-13: 978-0521813075
• Product Dimensions: 10 x 6.9 x 0.7 inches
• Shipping Weight: 1.2 pounds
• Average Customer Review: 4.7 out of 5 stars  See all reviews (3 customer reviews)
• Amazon Best Sellers Rank: #3,355,203 in Books (See Top 100 in Books)

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14 of 14 people found the following review helpful:

5.0 out of 5 stars Thin but useful, October 30, 2004

By 

wiredweird "wiredweird" (Earth, or somewhere nearby) - See all my reviews
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This review is from: Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences (Hardcover)

Don't let its small size (~200 pages) fool you. There's a lot of good material here, and in very usable form. In fact, that's the whole focus of the book: practical, efficient implementations.

The main topics, chapter by chapter, are simple matching of one desired word to a string, matching of multiple words, two levels of complexity in wildcards and regular expressions, and approximate matching. A number of important and historical algorithms are discussed in each chapter, in great detail. There's pseudo-code for the most important algorithms. Quite a few also have examples worked in detail. The mechanics are tedious and somewhat bulky, but anyone actually trying to implement these techniques will appreciate the examples.

What's really interesting is what's not in this book. You won't find a lot of theory, and you won't find some of the most famous algorithms in string matching. The authors make it clear that this is about practical algorithms with efficient implementations. Lots of the algorithms beloved by theoreticians are impractically complex or just plain slow. Those may be mentioned in passing or as the base for more practical algorithms, but are not welcome on these pages.

It's not an easy read, but it's not a book for people with easy problems. It discusses tradeoffs, like when one technique works well for short strings but another works better on long strings. It addresses the different needs of English-language processing and bioinformatics - just the different numbers of letters in each alphabet make a difference, in some cases.

This is a good one for anyone who takes string processing seriously. There's no cut&paste code here, but plenty for a knowledgable programmer to use. Even better, it offers references to the literature and to working code, and pointers to some books on related topics. I expect to get a lot of use out of this one.

//wiredweird

6 of 7 people found the following review helpful:

4.0 out of 5 stars Solid Theory, June 4, 2003

By 

Stephen Gould (Sydney, Australia (sometimes Palo Alto, USA)) - See all my reviews
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This review is from: Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences (Hardcover)

This is an excellent book for someone with a strong foundation in computer science wanting to learn about regular expression and string matching. It is not for the feint-hearted, and would not be recommended to computer science novices. Written by one of the world experts in the field, the relatively thin book is packed with theory and comments on application. The algorithms are presented in a very concise form which often requires a fair amount of thought when trying to implement. However once understood, the book makes an excellent reference for the various algorithms.

5.0 out of 5 stars Definitive. Period, September 23, 2011

By 

Mischa Sandberg (Vancouver, Canada) - See all my reviews
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This review is from: Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences (Paperback)

There was Knuth. And now there's Navarro. Every abstract string searching algorithm you'd care to understand, and implement, is carefully explained and analyzed, across domains ranging from DNA sequencing (the ACGT alphabet) through real-world text searching. From simple algorithms like Horspool, to complex FSA algoriths like Backward-DAWG, this book covers it all. I would be surprised if this book doesn't motivate you to work out a better string search, in your own field and context.