Part I: Introduction
Part II: Theory
Chapter 2. Biological Sequences
Chapter 4. Sequence Similarity
Part III: Practice
Chapter 6. Anatomy of a BLAST Report
Chapter 7. A BLAST Statistics Tutorial
Chapter 8. 20 Tips to Improve Your BLAST Searches
Part IV: Industrial-Strength BLAST
Chapter 10. Installation and Command-Line Tutorial
Chapter 12. Hardware and Software Optimizations
Part V: BLAST Reference
Chapter 13. NCBI-BLAST Reference
Chapter 14. WU-BLAST Reference
Part VI: Appendixes
Appendix A. NCBI Display Formats
Appendix B. Nucleotide Scoring Schemes
Appendix C. NCBI-BLAST Scoring Schemes