From coding theory to efficient pattern matching
SODA '09 Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms
Pattern matching with don't cares and few errors
Journal of Computer and System Sciences
ESA'07 Proceedings of the 15th annual European conference on Algorithms
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
A filtering algorithm for k-mismatch with don't cares
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Information Processing Letters
A filtering algorithm for k-mismatch with don't cares
Information Processing Letters
Finding the position of the k-mismatch and approximate tandem repeats
SWAT'06 Proceedings of the 10th Scandinavian conference on Algorithm Theory
A randomized numerical aligner (rNA)
LATA'10 Proceedings of the 4th international conference on Language and Automata Theory and Applications
A bibliography on computational molecular biology and genetics
Mathematical and Computer Modelling: An International Journal
Pattern matching in multiple streams
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
A randomized Numerical Aligner (rNA)
Journal of Computer and System Sciences
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Consider the string matching problem where differences between characters of the pattern and characters of the text are allowed. Each difference is due to either a mismatch between a character of the text and a character of the pattern or a superfluous character in the text or a superfluous character in the pattern. Given a text of length n, a pattern of length m and an integer k, we present an algorithm for finding all occurrences of the pattern in the text, each with at most k differences. The algorithm runs in O(m2 + k2n) time. Given the same input we also present an algorithm for finding all occurrences of the pattern in the text, each with at most k mismatches (superfluous characters in either the text or the pattern are not allowed). This algorithm runs in O(k(m logm + n)) time.