BLAST

This is the Title of the Book, eMatter Edition

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

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Preface

A Little Math, a Little Perl

Certain parts of this book are mathematical or algorithmic in nature, so you will find

various equations and computer programs throughout the book. If these notations

are unfamiliar to you, don’t panic. To make this book accessible to a general audi-

ence, we have included graphical examples and descriptive text along with the equa-

tions. The programming examples are written in Perl, one of the most popular

programming languages and one that has an especially strong following in bioinfor-

matics. While we could have relied on pseudocode for our examples, using a real lan-

guage means that you can run the programs on your own computer and edit them as

you wish.

Conventions Used in This Book

The following conventions are used in this book:

Constant width

Used for Perl programs, parameters, and BLAST output

Italics

Used for program names, databases, for emphasis, and for new terms where they

are defined

URLs Referenced in This Book

For more information about the URLs referenced in this book and for additional

material about BLAST, see this book’s web page, which is listed in the next section.

Comments and Questions

Please address comments and questions concerning this book to the publisher:

O’Reilly & Associates, Inc.

1005 Gravenstein Highway North

Sebastopol, CA 95472

[phone] (in the United States or Canada)

[phone] (international or local)

[phone] (fax)

There is a web page for this book, which lists errata, examples, or any additional

information. You can access this page at:

http://www.oreilly.com/catalog/blast