Self-indexing Based on LZ77

We introduce the first self-index based on the Lempel-Ziv 1977 compression format (LZ77). It is particularly competitive for highly repetitive text collections such as sequence databases of genomes of related species, software repositories, versioned document collections, and temporal text databases...

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Bibliographic Details
Published inCombinatorial Pattern Matching pp. 41 - 54
Main Authors Kreft, Sebastian, Navarro, Gonzalo
Format Book Chapter
LanguageEnglish
Published Berlin, Heidelberg Springer Berlin Heidelberg
SeriesLecture Notes in Computer Science
Subjects
Binary Search
Phrase Boundary
Reverse Trie
Software Repository
Text Collection
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Summary:We introduce the first self-index based on the Lempel-Ziv 1977 compression format (LZ77). It is particularly competitive for highly repetitive text collections such as sequence databases of genomes of related species, software repositories, versioned document collections, and temporal text databases. Such collections are extremely compressible but classical self-indexes fail to capture that source of compressibility. Our self-index takes in practice a few times the space of the text compressed with LZ77 (as little as 2.5 times), extracts 1–2 million characters of the text per second, and finds patterns at a rate of 10–50 microseconds per occurrence. It is smaller (up to one half) than the best current self-index for repetitive collections, and faster in many cases.
Bibliography:Partially funded by Millennium Institute for Cell Dynamics and Biotechnology (ICDB), Grant ICM P05-001-F, Mideplan, Chile and, the first author, by Conicyt’s Master Scholarship.
ISBN:9783642214578
3642214576
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-642-21458-5_6