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Basic local alignment search tool (blast)
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Preface
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
2.2 Evolution
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
3.6 Variations
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
6.2 Alignments
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
Glossary
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