BLAST

Part I: Introduction Chapter 1. Hello BLAST Section 1.1. What Is BLAST? Section 1.2. Using NCBI-BLAST Section 1.3. Alternate Output Formats Section 1.4. Alternate Alignment Views Section 1.5. The Next Step Section 1.6. Further Reading Part II: Theory Chapter 2. Biological Sequences Section 2.1. The Central Dogma of Molecular Biology Section 2.2. Evolution Section 2.3. Genomes and Genes Section 2.4. Biological Sequences and Similarity Section 2.5. Further Reading Chapter 3. Sequence Alignment Section 3.1. Global Alignment: Needleman-Wunsch Section 3.2. Local Alignment: Smith-Waterman Section 3.3. Dynamic Programming Section 3.4. Algorithmic Complexity Section 3.5. Global Versus Local Section 3.6. Variations Section 3.7. Final Thoughts Section 3.8. Further Reading Chapter 4. Sequence Similarity Section 4.1. Introduction to Information Theory Section 4.2. Amino Acid Similarity Section 4.3. Scoring Matrices Section 4.4. Target Frequencies, lambda, and H Section 4.5. Sequence Similarity Section 4.6. Karlin-Altschul Statistics Section 4.7. Sum Statistics and Sum Scores Section 4.8. Further Reading Part III: Practice Chapter 5. BLAST Section 5.1. The Five BLAST Programs Section 5.2. The BLAST Algorithm Section 5.3. Further Reading Chapter 6. Anatomy of a BLAST Report Section 6.1. Basic Structure Section 6.2. Alignments Chapter 7. A BLAST Statistics Tutorial Section 7.1. Basic BLAST Statistics Section 7.2. Using Statistics to Understand BLAST Results Section 7.3. Where Did My Oligo Go? Chapter 8. 20 Tips to Improve Your BLAST Searches Section 8.1. Don't Use the Default Parameters Section 8.2. Treat BLAST Searches as Scientific Experiments Section 8.3. Perform Controls, Especially in the Twilight Zone Section 8.4. View BLAST Reports Graphically Section 8.5. Use the Karlin-Altschul Equation to Design Experiments Section 8.6. When Troubleshooting, Read the Footer First Section 8.7. Know When to Use Complexity Filters Section 8.8. Mask Repeats in Genomic DNA Section 8.9. Segment Large Genomic Sequences Section 8.10. Be Skeptical of Hypothetical Proteins Section 8.11. Expect Contaminants in EST Databases Section 8.12. Use Caution When Searching Raw Sequencing Reads Section 8.13. Look for Stop Codons and Frame-Shifts to find Pseudo-Genes Section 8.14. Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX Section 8.15. Look for Gaps in Coverage as a Sign of Missed Exons Section 8.16. Parse BLAST Reports with Bioperl Section 8.17. Perform Pilot Experiments Section 8.18. Examine Statistical Outliers Section 8.19. Use links and topcomboN to Make Sense of Alignment Groups Section 8.20. How to Lie with BLAST Statistics Chapter 9. BLAST Protocols Section 9.1. BLASTN Protocols Section 9.2. BLASTP Protocols Section 9.3. BLASTX Protocols Section 9.4. TBLASTN Protocols Section 9.5. TBLASTX Protocols Part IV: Industrial-Strength BLAST Chapter 10. Installation and Command-Line Tutorial Section 10.1. NCBI-BLAST Installation Section 10.2. WU-BLAST Installation Section 10.3. Command-Line Tutorial Section 10.4. Editing Scoring Matrices Chapter 11. BLAST Databases Section 11.1. FASTA Files Section 11.2. BLAST Databases Section 11.3. Sequence Databases Section 11.4. Sequence Database Management Strategies Chapter 12. Hardware and Software Optimizations Section 12.1. The Persistence of Memory Section 12.2. CPUs and Computer Architecture Section 12.3. Compute Clusters Section 12.4. Distributed Resource Management Section 12.5. Software Tricks Section 12.6. Optimized NCBI-BLAST Part V: BLAST Reference Chapter 13. NCBI-BLAST Reference Section 13.1. Usage Statements Section 13.2. Command-Line Syntax Section 13.3. blastall Parameters Section 13.4. formatdb Parameters Section 13.5. fastacmd Parameters Section 13.6. megablast Parameters Section 13.7. bl2seq Parameters Section 13.8. blastpgp Parameters (PSI-BLAST and PHI-BLAST) Section 13.9. blastclust Parameters Chapter 14. WU-BLAST Reference Section 14.1. Usage Statements Section 14.2. Command-Line Syntax Section 14.3. WU-BLAST Parameters Section 14.4. xdformat Parameters Section 14.5. xdget Parameters Part VI: Appendixes Appendix A. NCBI Display Formats Section A.1. Brief Descriptions Section A.2. Detailed Descriptions and Examples Appendix B. Nucleotide Scoring Schemes Appendix C. NCBI-BLAST Scoring Schemes Section C.1. NCBI-BLAST Matrices and Gap Costs Appendix D. blast-imager.pl Appendix E. blast2table.pl Glossary Numbers A-G H-U Colophon Index [ Team LiB ]