Agrep — a Fast Approximate Pattern-matching Tool

Searching for a pattern in a text file is a very common operation in many applications ranging from text editors and databases to applications in molecular biology. In many instances the pattern does not appear in the text exactly. Errors in the text or in the query can result from misspelling or from experimental errors (e.g., when the text is a DNA sequence). The use of such approximate pattern matching has been limited until now to specific applications. Most text editors and searching programs do not support searching with errors because of the complexity involved in implementing it. In this paper we describe a new tool, called agrep, for approximate pattern matching. Agrep is based on a new efficient and flexible algorithm for approximate string matching. Agrep is also competitive with other tools for exact string matching; it include many options that make searching more powerful and convenient.