Fast relative Lempel-Ziv self-index for similar sequences

Abstract

Recent advances in biotechnology and web technology are generating huge collections of similar strings. People now face the problem of storing them compactly while supporting fast pattern searching. One compression scheme called relative Lempel-Ziv compression uses textual substitutions from a reference text as follows: Given a (large) set S of strings, represent each string in S as a concatenation of substrings from a reference string R. This basic scheme gives a good compression ratio when every string in S is similar to R, but does not provide any pattern searching functionality. Here, we describe a new data structure that supports fast pattern searching. © 2012 Springer-Verlag.