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