By Ian Korf, Mark Yandell, Joseph Bedell
1st Edition July 2003 
ISBN: 0-596-00299-8
360 pages,

Our Price: $39.95

Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power.

BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:

BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. This is a book that any biologist should own.

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Bioinformatics Books (Bioinformatics Books)

Foreword

Preface

Part I. Introduction

1. Hello BLAST
     What Is BLAST?
     Using NCBI-BLAST
     Alternate Output Formats
     Alternate Alignment Views
     The Next Step
     Further Reading

Part II. Theory

2. Biological Sequences
     The Central Dogma of Molecular Biology
     Evolution
     Genomes and Genes
     Biological Sequences and Similarity
     Further Reading

3. Sequence Alignment
     Global Alignment: Needleman-Wunsch
     Local Alignment: Smith-Waterman
     Dynamic Programming
     Algorithmic Complexity
     Global Versus Local
     Variations
     Final Thoughts
     Further Reading

4. Sequence Similarity
     Introduction to Information Theory
     Amino Acid Similarity
     Scoring Matrices
     Target Frequencies, lambda, and H
     Sequence Similarity
     Karlin-Altschul Statistics
     Sum Statistics and Sum Scores
     Further Reading

Part III. Practice

5. BLAST
     The Five BLAST Programs
     The BLAST Algorithm
     Further Reading

6. Anatomy of a BLAST Report
     Basic Structure
     Alignments

7. A BLAST Statistics Tutorial
     Basic BLAST Statistics
     Using Statistics to Understand BLAST Results
     Where Did My Oligo Go?

8. 20 Tips to Improve Your BLAST Searches
     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
     8.4 View BLAST Reports Graphically 118
     8.5 Use the Karlin-Altschul Equation to Design Experiments 119
     8.6 When Troubleshooting, Read the Footer First 119
     8.7 Know When to Use Complexity Filters 120
     8.8 Mask Repeats in Genomic DNA 121
     8.9 Segment Large Genomic Sequences 121
     8.10 Be Skeptical of Hypothetical Proteins 123
     8.11 Expect Contaminants in EST Databases 123
     8.12 Use Caution When Searching Raw Sequencing Reads 124
     8.13 Look for Stop Codons and Frame-Shifts to find Pseudo-Genes 124
     8.14 Consider Using Ungapped Alignment for BLASTX, TBLASTN, and               TBLASTX 124
     8.15 Look for Gaps in Coverage as a Sign of Missed Exons 126
     8.16 Parse BLAST Reports with Bioperl 126
     8.17 Perform Pilot Experiments 128
     8.18 Examine Statistical Outliers 128
     8.19 Use links and topcomboN to Make Sense of Alignment Groups 128
     8.20 How to Lie with BLAST Statistics 128

9. BLAST Protocols
     BLASTN Protocols
     BLASTP Protocols
     BLASTX Protocols
     TBLASTN Protocols
     TBLASTX Protocols

Part IV. Industrial-Strength BLAST

10. Installation and Command-Line Tutorial
     NCBI-BLAST Installation
     WU-BLAST Installation
     Command-Line Tutorial
     Editing Scoring Matrices

11. BLAST Databases
     FASTA Files
     BLAST Databases
     Sequence Databases
     Sequence Database Management Strategies

12. Hardware and Software Optimizations
     The Persistence of Memory
     CPUs and Computer Architecture
     Compute Clusters
     Distributed Resource Management
     Software Tricks
     Optimized NCBI-BLAST

Part V. BLAST Reference

13. NCBI-BLAST Reference
     Usage Statements
     Command-Line Syntax
     blastall Parameters
     formatdb Parameters
     fastacmd Parameters
     megablast Parameters
     bl2seq Parameters
     blastpgp Parameters (PSI-BLAST and PHI-BLAST)
     blastclust Parameters

14. WU-BLAST Reference
     Usage Statements
     Command-Line Syntax
     WU-BLAST Parameters
     xdformat Parameters
     xdget Parameters

Part VI. Appendixes

A. NCBI Display Formats

B. Nucleotide Scoring Schemes

C. NCBI-BLAST Scoring Schemes

D. blast-imager.pl

E. blast2table.pl

Glossary

Index