Text Searching and Indexing

Although data is stored in various ways, text remains the main form of exchanging information. This is particularly evident in literature or linguistics where data is composed of huge corpora and dictionaries. This applies as well to computer science, where a large amount of data is stored in linear files. And this is also the case in molecular biology where biological molecules can often be approximated as sequences of nucleotides or amino acids. Moreover, the quantity of available data in this fields tends to double every 18 months. This is the reason why algorithms should be efficient even if the speed of computers increases at a steady pace. Pattern matching is the problem of locating a specific pattern inside raw data. The pattern is usually a collection of strings described in some formal language. In this chapter we present several algorithms for solving the problem when the pattern is composed of a single string. In several applications, texts need to be structured before being searched. Even if no further information is known about their syntactic structure, it is possible and indeed extremely efficient to build a data structure that support searches. In this chapter we present suffix arrays, suffix trees, suffix automata and compact suffix automata.