Wed, 20 Aug 2008 21:27:15 BST CiteULike: nedwards's inexact-string-matching http://www.citeulike.org/user/nedwards/tag/inexact-string-matching CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/nedwards/article/163533 <i>(15 January 1997)</i><br /><br />Traditionally an area of study in computer science, string algorithms have, in recent years, become an increasingly important part of biology, particularly genetics. This volume is a comprehensive look at computer algorithms for string processing. In addition to pure computer science, Gusfield adds extensive discussions on biological problems that are cast as string problems and on methods developed to solve them. This text emphasizes the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology Dan Gusfield (15 January 1997) 2005-04-18T14:43:31-00:00 1997 Cambridge University Press inexact-string-matching sequence-alignment string-indexing string-matching suffix-trees http://www.citeulike.org/user/nedwards/article/332260 <i>Bioinformatics, Vol. 18, No. 3. (March 2002), pp. 440-445.</i><br /><br />MOTIVATION: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. RESULTS: We present a new homology search algorithm 'PatternHunter' that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop. AVAILABILITY: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free. PatternHunter: faster and more sensitive homology search. B Ma J Tromp M Li doi:10.1093/bioinformatics/18.3.440 Bioinformatics, Vol. 18, No. 3. (March 2002), pp. 440-445. 2005-09-26T01:46:36-00:00 2002 Bioinformatics 1367-4803 18 3 440 445 gapped-seeds inexact-string-matching locality-sensitive-hashing sequence-alignment string-indexing string-matching http://www.citeulike.org/user/nedwards/article/1572534 <i>SIAM J. Comput., Vol. 22, No. 2. (April 1993), pp. 243-260.</i> Approximate Boyer-Moore string matching Jorma Tarhio Esko Ukkonen doi:10.1137/0222018 SIAM J. Comput., Vol. 22, No. 2. (April 1993), pp. 243-260. 2007-08-17T13:57:47-00:00 1993 SIAM J. Comput. 0097-5397 22 2 243 260 Society for Industrial and Applied Mathematics inexact-string-matching sequence-alignment string-matching http://www.citeulike.org/user/nedwards/article/1374065 <i>(2006), pp. 1203-1212.</i> Efficient algorithms for substring near neighbor problem Alexandr Andoni Piotr Indyk doi:10.1145/1109557.1109690 (2006), pp. 1203-1212. 2007-06-09T07:29:51-00:00 2006 1203 1212 ACM Press inexact-string-matching locality-sensitive-hashing string-matching