Faster algorithms for string matching with k mismatches

The string matching with mismatches problem is that of finding the number of mismatches between a pattern P of length m and every length m substring of the text  T. Currently, the fastest algorithms for this problem are the following. The Galil–Giancarlo algorithm finds all locations where the patte...

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Veröffentlicht in:Journal of algorithms Jg. 50; H. 2; S. 257 - 275
Hauptverfasser: Amir, Amihood, Lewenstein, Moshe, Porat, Ely
Format: Journal Article Tagungsbericht
Sprache:Englisch
Veröffentlicht: San Diego, CA Elsevier Inc 01.02.2004
Elsevier
Schlagworte:
Algorithmics. Computability. Computer arithmetics
Applied sciences
Approximate string matching
Combinatorial algorithms on words
Computer science; control theory; systems
Design and analysis of algorithms
Exact sciences and technology
Hamming distance
Theoretical computing
Hamming distance
Approximate string matching
Combinatorial algorithms on words
Design and analysis of algorithms
Error estimation
Computer theory
Algorithm
Mismatching
String matching
ISSN:0196-6774, 1090-2678
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Zusammenfassung:The string matching with mismatches problem is that of finding the number of mismatches between a pattern P of length m and every length m substring of the text  T. Currently, the fastest algorithms for this problem are the following. The Galil–Giancarlo algorithm finds all locations where the pattern has at most k errors (where k is part of the input) in time O( nk). The Abrahamson algorithm finds the number of mismatches at every location in time O(n m logm ) . We present an algorithm that is faster than both. Our algorithm finds all locations where the pattern has at most k errors in time O(n k logk ) . We also show an algorithm that solves the above problem in time O(( n+( nk 3)/ m)log k).
ISSN:0196-6774
1090-2678
DOI:10.1016/S0196-6774(03)00097-X