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
