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Abstract: The problem of fast searching of a pattern that contains Classes of characters and Bounded size Gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site is associated with the CBG [RK] \Gamma x(2; 3) \Gamma [DE] \Gamma x(2; 3) \Gamma Y , where the brackets match any of the letters inside, and x(2; 3) a gap of length between 2 and 3). Currently, the only way to search a CBG in a text is to convert... (Update)
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BibTeX entry: (Update)
G. Navarro and M. Ranot. Fast and simple character classes and bounded gaps pattern matching, with application to protein searching. In Proceedings of the 5th Annual International Conference on Computational Molecular Biology (RECOMB), pages 231-240. ACM Press, 2001. http://citeseer.ist.psu.edu/article/navarro01fast.html More
@inproceedings{ navarro01fast,
author = "Gonzalo Navarro and Mathieu Raffinot",
title = "Fast and simple character classes and bounded gaps pattern matching, with application to protein searching",
booktitle = "{RECOMB}",
pages = "231-240",
year = "2001",
url = "citeseer.ist.psu.edu/article/navarro01fast.html" }
Citations (may not include all citations):81 A new approach to text searching (context) - Baeza-Yates, Gonnet - 1992
64 From regular expression to deterministic automata (context) - Berry, Sethi - 1986
28 Regular expressions into finite automata (context) - Bruggemann-Klein - 1993
24 Text retrieval: Theory and practice (context) - Baeza-Yates - 1992
24 Faster approximate string matching - Baeza-Yates, Navarro - 1999
14 A generalized profile syntax for biomolecular sequences moti.. (context) - Bucher, Bairoch - 1994
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