If you like definition-theorem-proof-example and exercise books, Gusfield's book is the definitive text for string algorithms. The algorithms are abstracted from their biological applications, and the book would make sense without reading a single page of the biological motivations. Gusfield aims his book at readers who are fluent in basic algorithms and data structures (at the level of Cormen, Leisersohn and Rivest's excellent text). The exercises are wonderfully illustrative, being neither trivial nor impossible.
All of the major exact string algorithms are covered, including Knuth-Morris-Pratt, Boyer-Moore, Aho-Corasick and the focus of the book, suffix trees for the much harder probem of finding all repeated substrings of a given string in linear time. In addition to exact string matching, there are extensive discussions of inexact matching. Even the discussions of widely known topics like dynamic programming for edit distance are insightful; for instance, we find how to easily cut space requirements from quadratic to linear. There is also a short chapter on semi-numerical matching methods, which are also of use in information retrieval applications. Inexact matching is extended to the threshold all-against-all problem, which finds all substrings of a string that match up to a given edit distance threshold. The theoretical development concludes with the much more difficult problem of aligning multiple sequences with ultrametric trees, with applications to phylogenetic alignment for evolutionary trees (an approach that has also been applied to the evolution of natural languages).
Note that there is no discussion of statistical string matching. For that, Durbin, Eddy, Krogh and Mitchison's "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acides" is a good choice, or for those more interested in language than biology, Manning and Schuetze's "Statistical Natural Language Processing". There is also no information on more structured string matching models such as context-free grammars, as are commonly used to analyze RNA folding or natural language syntax. Luckily, Durbin et al. and Manning and Schuetze also provide excellent coverage of these higher-order models in their books.
This book is not about efficient implementation. If you need to build these algorithms, you'll also need to know how to write efficient code and tune it for your needs. This is an algorithms book, pure and simple.
As a computer scientist, I found the discussions of computational biology to be more enlightening than in other textbooks on similar topics such as Durbin et al., because Gusfield does not assume the reader has any background in cellular biology. Instead, he provides his own clear and gentle introductions illustrated with algorithms, applications, open problems and extensive references. Like most Cambridge University Press books, this one is beautifully typeset and edited.
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Bob Carpenter
Definitive String Algorithms Text
2003年1月5日 -
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L. Leonard
Great algorithms book mostly on strings
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Santiago Pineda Montoya
Excelente condición
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Santiago Pineda Montoya
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Shane Li
very good seller
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Alankar K.
Product as expected
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