On string matching in chunked texts

Authors:
Hannu Peltola;Jorma Tarhio
Affiliations:
Department of Computer Science and Engineering, Helsinki University of Technology, Finland;Department of Computer Science and Engineering, Helsinki University of Technology, Finland
Venue:
CIAA'07 Proceedings of the 12th international conference on Implementation and application of automata
Year:
2007

Citing 9
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Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences

Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences

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Abstract

We study exact string matching in special texts, which consist of consecutive fixed-length chunks where each position of a chunk has a character distribution of its own. This kind of setting can also be interpreted so that a chunk represents a character of a larger alphabet. If texts and patterns are of this kind, it may ruin the efficiency of common algorithms. We examine anomalies related to the Horspool and Sunday algorithms in this setting. In addition we present two new algorithms.