See also

Home
Misc
Basic local alignment search tool (blast)

Glossary

Glossary

Numbers

A-G

H-U

Audience for This Book

Structure of This Book

A Little Math, a Little Perl

Conventions Used in This Book

URLs Referenced in This Book

Comments and Questions

Acknowledgments

Part I: Introduction

Chapter 1. Hello BLAST

1.1 What Is BLAST?

1.2 Using NCBI-BLAST

1.3 Alternate Output Formats

1.4 Alternate Alignment Views

1.5 The Next Step

1.6 Further Reading

Part II: Theory

Chapter 2. Biological Sequences

2.1 The Central Dogma of Molecular Biology

2.3 Genomes and Genes

2.4 Biological Sequences and Similarity

2.5 Further Reading

Chapter 3. Sequence Alignment

3.1 Global Alignment: Needleman-Wunsch

3.2 Local Alignment: Smith-Waterman

3.3 Dynamic Programming

3.4 Algorithmic Complexity

3.5 Global Versus Local

3.7 Final Thoughts

3.8 Further Reading

Chapter 4. Sequence Similarity

4.1 Introduction to Information Theory

4.2 Amino Acid Similarity

4.3 Scoring Matrices

4.4 Target Frequencies, lambda, and H

4.5 Sequence Similarity

4.6 Karlin-Altschul Statistics

4.7 Sum Statistics and Sum Scores

4.8 Further Reading

Part III: Practice

Chapter 5. BLAST

5.1 The Five BLAST Programs

5.2 The BLAST Algorithm

5.3 Further Reading

Chapter 6. Anatomy of a BLAST Report

6.1 Basic Structure

Chapter 7. A BLAST Statistics Tutorial

7.1 Basic BLAST Statistics

7.2 Using Statistics to Understand BLAST Results

7.3 Where Did My Oligo Go?

Chapter 8. 20 Tips to Improve Your BLAST Searches

8.1 Don't Use the Default Parameters

8.2 Treat BLAST Searches as Scientific Experiments

8.3 Perform Controls, Especially in the Twilight Zone

8.4 View BLAST Reports Graphically

8.5 Use the Karlin-Altschul Equation to Design Experiments

8.6 When Troubleshooting, Read the Footer First

8.7 Know When to Use Complexity Filters

8.8 Mask Repeats in Genomic DNA

8.9 Segment Large Genomic Sequences

8.10 Be Skeptical of Hypothetical Proteins

8.11 Expect Contaminants in EST Databases

8.12 Use Caution When Searching Raw Sequencing Reads

8.13 Look for Stop Codons and Frame-Shifts to find Pseudo-Genes

8.14 Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX

8.15 Look for Gaps in Coverage as a Sign of Missed Exons

8.16 Parse BLAST Reports with Bioperl

8.17 Perform Pilot Experiments

8.18 Examine Statistical Outliers

8.19 Use links and topcomboN to Make Sense of Alignment Groups

8.20 How to Lie with BLAST Statistics

Chapter 9. BLAST Protocols

9.1 BLASTN Protocols

9.2 BLASTP Protocols

9.3 BLASTX Protocols

9.4 TBLASTN Protocols

9.5 TBLASTX Protocols

Part IV: Industrial-Strength BLAST

Chapter 10. Installation and Command-Line Tutorial

10.1 NCBI-BLAST Installation

10.2 WU-BLAST Installation

10.3 Command-Line Tutorial

10.4 Editing Scoring Matrices

Chapter 11. BLAST Databases

11.1 FASTA Files

11.2 BLAST Databases

11.3 Sequence Databases

11.4 Sequence Database Management Strategies

Chapter 12. Hardware and Software Optimizations

12.1 The Persistence of Memory

12.2 CPUs and Computer Architecture

12.3 Compute Clusters

12.4 Distributed Resource Management

12.5 Software Tricks

12.6 Optimized NCBI-BLAST

Part V: BLAST Reference

Chapter 13. NCBI-BLAST Reference

13.1 Usage Statements

13.2 Command-Line Syntax

13.3 blastall Parameters

13.4 formatdb Parameters

13.5 fastacmd Parameters

13.6 megablast Parameters

13.7 bl2seq Parameters

13.8 blastpgp Parameters (PSI-BLAST and PHI-BLAST)

13.9 blastclust Parameters

Chapter 14. WU-BLAST Reference

14.1 Usage Statements

14.2 Command-Line Syntax

14.3 WU-BLAST Parameters

14.4 xdformat Parameters

14.5 xdget Parameters

Part VI: Appendixes

Appendix A. NCBI Display Formats

A.1 Brief Descriptions

A.2 Detailed Descriptions and Examples

Appendix B. Nucleotide Scoring Schemes

Appendix C. NCBI-BLAST Scoring Schemes

C.1 NCBI-BLAST Matrices and Gap Costs

Appendix D. blast-imager.pl

Appendix E. blast2table.pl

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