BLAST

This is the Title of the Book, eMatter Edition

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

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Preface

growing orbit. So if you’ve recently become interested in bioinformatics, understand-

ing BLAST is a great place to start. And if you’re already a bioinformatics student or

professional, this book can help you get more out of BLAST.

Structure of This Book

This book is divided into six parts: An Introduction to BLAST, Theory, Practice,

Industrial-Strength BLAST, Reference, and the Appendixes. The quick start guide in

Chapter 1 is the best place to begin if you’ve never run BLAST before. You won’t

need sophisticated hardware or software, just a web browser connected to the Inter-

net. In Part II, we begin by exploring the molecular biology, computer science, and

statistics that form the foundation of BLAST searches. We then describe the BLAST

algorithm in detail. You will find that a sound theoretical understanding is essential

when you put BLAST into practice. In Part III, we present practical advice to help

you design and interpret BLAST experiments intelligently and efficiently. Whether

you’re a complete novice or a seasoned pro, you’ll find the tutorials and protocols a

valuable resource. Part IV discusses using BLAST in a high-throughput setting where

the goal is to get as much BLAST as possible for your buck. Here, we integrate the

information usually found scattered