BLAST

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