LZ77-Based self-indexing with faster pattern matching

Abstract

To store and search genomic databases efficiently, researchers have recently started building self-indexes based on LZ77. As the name suggests, a self-index for a string supports both random access and pattern matching queries. In this paper we show how, given a string S[1..n] whose LZ77 parse consists of z phrases, we can store a self-index for S in O(z log(n/z)) space such that later, first, given a position i and a length l, we can extract S[i..i + l ? 1] in O(l + log n) time; second, given a pattern P[1..m], we can list the occ occurrences of P in S in O(mlogm+ occ log log n) time. © 2014 Springer-Verlag Berlin Heidelberg.