Modern BLAST Programs

Abstract

The Basic Local Alignment Search Tool (BLAST) is arguably the most widely used program in bioinformatics. By sacrificing sensitivity for speed, it makes sequence comparison practical on huge sequence databases currently available. The original version of BLAST was developed in 1990. Since then it has spawned a variant of specialized programs. This chapter surveys the development of BLAST and BLAST-like programs for homology search, discusses alignment statistics that are used in assessment of reported matches in BLAST, and provides the reader with guidance to select appropriate programs and set proper parameters to match research requirements.