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