BLAST

This is the Title of the Book, eMatter Edition

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

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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 ...