BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

3

Chapter 1

CHAPTER 1

Hello BLAST

Welcome to BLAST! This chapter offers a quick start guide to BLAST by exploring

some Internet search pages. Throughout the chapter, you may encounter unfamiliar

(or even frightening) terms. Don’t panic. The terms are fully explained in later chap-

ters or in the Glossary. You don’t need to understand all the concepts to get the most

out of this chapter. If you’re already a seasoned BLAST user, feel free to skip this

introduction and dive right into the later sections.

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 sev-

eral 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 rig-

orous 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 com-

mercial. 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.