BLAST

v

Table of Contents

Foreword

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xi

Preface

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Part I. Introduction

1. Hello BLAST

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3

What Is BLAST? 3

Using NCBI-BLAST 4

Alternate Output Formats 12

Alternate Alignment Views 13

The Next Step 14

Further Reading 15

Part II. Theory

2. Biological Sequences

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19

The Central Dogma of Molecular Biology 19

Evolution 27

Genomes and Genes 35

Biological Sequences and Similarity 38

Further Reading 39

3. Sequence Alignment

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40

Global Alignment: Needleman-Wunsch 40

Local Alignment: Smith-Waterman 46

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Dynamic Programming 50

Algorithmic Complexity 50

Global Versus Local 50

Variations 51

Final Thoughts 53

Further Reading 53

4. Sequence Similarity

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55

Introduction to Information Theory 55

Amino Acid Similarity 57

Scoring Matrices 59

Target Frequencies, lambda, and H 60

Sequence Similarity 64

Karlin-Altschul Statistics 65

Sum Statistics and Sum Scores 67

Further Reading 70

Part III. Practice

5. BLAST

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75

The Five BLAST Programs 75

The BLAST Algorithm 76

Further Reading 87

6. Anatomy of a BLAST Report

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88

Basic Structure 88

Alignments 90

7. A BLAST Statistics Tutorial

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Basic BLAST Statistics 96

Using Statistics to Understand BLAST Results 109

Where Did My Oligo Go? 109

8. 20 Tips to Improve Your BLAST Searches

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116

8.1 Don’t Use the Default Parameters 116

8.2 Treat BLAST Searches as Scientific Experiments 116

8.3 Perform Controls, Especially in the Twilight Zone 117