Succinct gapped suffix arrays

Authors:
Luís M. S. Russo;German Tischler
Affiliations:
Instituto Superior Técnico-Universidade Técnica de Lisboa, Lisboa and INESC-ID, Knowledge Discovery and Bioinformatics Group, Lisbon, Portugal;Lehrstuhl für Informatik II, Universität Würzburg, Würzburg, Germany
Venue:
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Year:
2011

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Abstract

Gapped suffix arrays (also known as bi-factor arrays) were recently presented for approximate searching under the Hamming distance. These structures can be used to find occurrences of a pattern P, where the characters inside a gap do not have to match. This paper describes a succinct representation of gapped suffix arrays.