1.1 What Is BLAST?

BLAST is an acronym for Basic Local Alignment Search Tool. Despite the adjective "Basic" in its name, BLAST is a sophisticated software package that has become the single most important piece of software in the field of bioinformatics. There are several reasons for this. First, sequence similarity is a powerful tool for identifying the unknowns in the sequence world. Second, BLAST is fast. The sequence world is big and growing rapidly, so speed is important. Third, BLAST is reliable, from both a rigorous statistical standpoint and a software development point of view. Fourth, BLAST is flexible and can be adapted to many sequence analysis scenarios. Finally, BLAST is entrenched in the bioinformatics culture to the extent that the word "blast" is often used as a verb. There are other BLAST-like algorithms with some useful features, but the historical momentum of BLAST maintains its popularity above all others.

Although BLAST originated at the National Center for Biotechnology Information (NCBI), its development continues at various institutions, both academic and commercial. This can be a little confusing, especially because people often put prefixes or suffixes on the acronym to come up with names like XYZ-BLAST-PDQ. We have aimed to keep this book as simple as possible, and therefore we concentrate on the two most popular versions: NCBI-BLAST and WU-BLAST (pronounced "woo blast"). NCBI-BLAST, as the name suggests, is the version available from the NCBI. WU-BLAST comes from Washington University in St. Louis and is developed by Warren Gish, one of the original authors of BLAST.