This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity. Several Web-based and stand-alone implementations are reviewed, and key features of typical search results are discussed.
Specifically, this Guide introduces concepts and theories that underpin the BLAST search tool, and examines features of search outputs important for understanding and interpreting BLAST results. On reading this Guide, users will be able to: i) search a variety of Web-based sequence databases with different query sequences, and alter search parameters; ii) explain a range of typical search parameters, and the likely impacts on search outputs of changing them; iii) analyse the information conveyed in search outputs and infer the significance of reported matches; iv) examine and investigate the annotations of reported matches, and their provenance; and v) compare the outputs of different BLAST implementations and evaluate the implications of any differences.