Fixed Block Compression Boosting in FM-Indexes: Theory and Practice

The FM index (Ferragina and Manzini in J ACM 52(4):552–581, 2005 ) is a widely-used compressed data structure that stores a string T in a compressed form and also supports fast pattern matching queries. In this paper, we describe new FM-index variants that combine nice theoretical properties, simple...

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Published in:Algorithmica Vol. 81; no. 4; pp. 1370 - 1391
Main Authors: Gog, Simon, Kärkkäinen, Juha, Kempa, Dominik, Petri, Matthias, Puglisi, Simon J.
Format: Journal Article
Language:English
Published: New York Springer US 01.04.2019
Springer Nature B.V
Subjects:
Algorithm Analysis and Problem Complexity
Algorithms
Computer Science
Computer Systems Organization and Communication Networks
Data storage
Data structures
Data Structures and Information Theory
Mathematics of Computing
Pattern matching
Performance indices
Theory of Computation
Wavelet analysis
Text indexing
Compression boosting
FM-index
Wavelet tree
Suffix array
Pattern matching
ISSN:0178-4617, 1432-0541
Online Access:Get full text
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Summary:The FM index (Ferragina and Manzini in J ACM 52(4):552–581, 2005 ) is a widely-used compressed data structure that stores a string T in a compressed form and also supports fast pattern matching queries. In this paper, we describe new FM-index variants that combine nice theoretical properties, simple implementation and improved practical performance. Our main theoretical 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. We also describe several new techniques for implementing fixed-block boosting efficiently, including a new, fast, and space-efficient implementation of wavelet trees. Our extensive experiments show the new indexes to be consistently fast and small relative to the state-of-the-art, and thus they make a good “off-the-shelf” choice for many applications.
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ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-018-0475-9