Full-Text Indexes in External Memory

A full-text index is a data structure storing a text (a string or a set of strings) and supporting string matching queries: Given a pattern string P, find all occurrences of P in the text. The best-known full-text index is the suffix tree [761], but numerous others have been developed. Due to their fast construction and the wealth of combinatorial information they reveal, full-text indexes (and suffix trees in particular) also have many uses beyond basic string matching. For example, the number of distinct substrings of a string or the longest common substrings of two strings can be computed in linear time [231]. Gusfield [366] describes several applications in computational biology, and many others are listed in [359].