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Self-indexing based on LZ77. (English) Zbl 1339.68334
Giancarlo, Raffaele (ed.) et al., Combinatorial pattern matching. 22nd annual symposium, CPM 2011, Palermo, Italy, June 27–29, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-21457-8/pbk). Lecture Notes in Computer Science 6661, 41-54 (2011).
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.
For the entire collection see [Zbl 1216.68028].

68W32 Algorithms on strings
68P15 Database theory
68P30 Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science)
92D10 Genetics and epigenetics
Full Text: DOI
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