Cambridge Core – Computational Biology and Bioinformatics – Algorithms on Strings, Trees, and Sequences – by Dan Gusfield. Dan Gusfield, Suffix Trees (and Relatives) Come of Age in Bioinformatics, Proceedings of the IEEE Computer Society Conference on Bioinformatics, p.3, August. Pris: kr. Inbunden, Skickas inom vardagar. Köp Algorithms on Strings, Trees, and Sequences av Dan Gusfield på
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To get the free app, enter your mobile phone number. Would you like to tell us about a lower price? 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 ny pure computer science, the book sequencs 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.
Algorihtms approaches to this complex material simplify methods that up to now have been for the specialist alone.
With over exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in sequwnces science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals. Read more Read less. Discover Prime Book Box for Kids.
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yb Editorial Reviews Review ” It will hopefully encourage them to question the importance of the problems they endeavor to solve.
Also found in the text are interesting biological examples of sequence analysis In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data produced by various genome projects. This book explains a wide range of computer methods for string processing. It also contains extensive discussions on biological problems that are cast as aequences problems, and on techniques to solve them. The book sequeces both a reference for computer scientists and computer-oriented professionals in biology and bio-informatics and a textbook for graduate and advanced undergraduate courses on string algorithms and on computational biology.
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Showing of 16 reviews. Top Reviews Most recent Top Reviews. There was a problem filtering reviews right now. Please try again later. If you like seuqences 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 ran 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 apgorithms also dah 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 algorithsm 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. Probabilistic Models of Proteins and Nucleic Acides” is a good choice, or sdquences 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 alogrithms or natural language syntax.
Luckily, Durbin et al. This book is not about efficient implementation.
Algorithms on Strings, Trees, and Sequences (Gusfield) – Wiki
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. Instead, he gusfidld 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. A well written text book with an obvious bias to biological application, but maybe most useful for its clear explanation and rigour of string algorithms.
The book is very accessible for clearly and concisely describing the challenging algorithms it presents. It is a great tool for learning the algorithms necessary for effective software design sequencse bioinformatics.
One person found this helpful. Without doubt this book is the best book about string algorithms, and sometime far beyond that. It will definitely change the way of your thinking. Don’t get thrown off by the ‘bio’ in the title. I use it for computer security – signature based intrusion detection.
This is a very dense book for the serious. The author does not waste any time on trivialities. Algorkthms gives a brief orientation to the notations and jumps into very intricate algorithms right from the start.
You will need to draw pictures or make oh on a scratch paper as you read to follow concepts from one paragraph to the next. This is a treatise on string algorithms. See all 16 reviews.
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