Fixed block compression boosting in FM-indexes

Authors:
Juha Kärkkäinen;Simon J. Puglisi
Affiliations:
Department of Computer Science, University of Helsinki, Finland;Department of Informatics, King's College London, London, United Kingdom
Venue:
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Year:
2011

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Abstract

A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text. Among the best compressed self-indexes, in theory and in practice, are several members of the FMindex family. In this paper, we describe new FM-index variants that combine nice theoretical properties, simple implementation and improved practical performance. Our main result is a new technique called fixed block compression boosting, which is a simpler and faster alternative to optimal compression boosting and implicit compression boosting used in previous FM-indexes.