BLAST
BLAST By Ian Korf, Mark Yandell, Joseph Bedell
July 2003
Pages: 360

| Table of Contents | Index | Sample Chapter | Colophon

Table of Contents

  1. Introduction

    1. Chapter 1 Hello BLAST

      1. What Is BLAST?
      2. Using NCBI-BLAST
      3. Alternate Output Formats
      4. Alternate Alignment Views
      5. The Next Step
      6. Further Reading

  2. Theory

    1. Chapter 2 Biological Sequences

      1. The Central Dogma of Molecular Biology
      2. Evolution
      3. Genomes and Genes
      4. Biological Sequences and Similarity
      5. Further Reading

    2. Chapter 3 Sequence Alignment

      1. Global Alignment: Needleman-Wunsch
      2. Local Alignment: Smith-Waterman
      3. Dynamic Programming
      4. Algorithmic Complexity
      5. Global Versus Local
      6. Variations
      7. Final Thoughts
      8. Further Reading

    3. Chapter 4 Sequence Similarity

      1. Introduction to Information Theory
      2. Amino Acid Similarity
      3. Scoring Matrices
      4. Target Frequencies, lambda, and H
      5. Sequence Similarity
      6. Karlin-Altschul Statistics
      7. Sum Statistics and Sum Scores
      8. Further Reading

  3. Practice

    1. Chapter 5 BLAST

      1. The Five BLAST Programs
      2. The BLAST Algorithm
      3. Further Reading

    2. Chapter 6 Anatomy of a BLAST Report

      1. Basic Structure
      2. Alignments

    3. Chapter 7 A BLAST Statistics Tutorial

      1. Basic BLAST Statistics
      2. Using Statistics to Understand BLAST Results
      3. Where Did My Oligo Go?

    4. Chapter 8 20 Tips to Improve Your BLAST Searches

      1. Don't Use the Default Parameters
      2. Treat BLAST Searches as Scientific Experiments
      3. Perform Controls, Especially in the Twilight Zone
      4. View BLAST Reports Graphically
      5. Use the Karlin-Altschul Equation to Design Experiments
      6. When Troubleshooting, Read the Footer First
      7. Know When to Use Complexity Filters
      8. Mask Repeats in Genomic DNA
      9. Segment Large Genomic Sequences
      10. Be Skeptical of Hypothetical Proteins
      11. Expect Contaminants in EST Databases
      12. Use Caution When Searching Raw Sequencing Reads
      13. Look for Stop Codons and Frame-Shifts to find Pseudo-Genes
      14. Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX
      15. Look for Gaps in Coverage as a Sign of Missed Exons
      16. Parse BLAST Reports with Bioperl
      17. Perform Pilot Experiments
      18. Examine Statistical Outliers
      19. Use links and topcomboN to Make Sense of Alignment Groups
      20. How to Lie with BLAST Statistics

    5. Chapter 9 BLAST Protocols

      1. BLASTN Protocols
      2. BLASTP Protocols
      3. BLASTX Protocols
      4. TBLASTN Protocols
      5. TBLASTX Protocols

  4. Industrial-Strength BLAST

    1. Chapter 10 Installation and Command-Line Tutorial

      1. NCBI-BLAST Installation
      2. WU-BLAST Installation
      3. Command-Line Tutorial
      4. Editing Scoring Matrices

    2. Chapter 11 BLAST Databases

      1. FASTA Files
      2. BLAST Databases
      3. Sequence Databases
      4. Sequence Database Management Strategies

    3. Chapter 12 Hardware and Software Optimizations

      1. The Persistence of Memory
      2. CPUs and Computer Architecture
      3. Compute Clusters
      4. Distributed Resource Management
      5. Software Tricks
      6. Optimized NCBI-BLAST

  5. BLAST Reference

    1. Chapter 13 NCBI-BLAST Reference

      1. Usage Statements
      2. Command-Line Syntax
      3. blastall Parameters
      4. formatdb Parameters
      5. fastacmd Parameters
      6. megablast Parameters
      7. bl2seq Parameters
      8. blastpgp Parameters (PSI-BLAST and PHI-BLAST)
      9. blastclust Parameters

    2. Chapter 14 WU-BLAST Reference

      1. Usage Statements
      2. Command-Line Syntax
      3. WU-BLAST Parameters
      4. xdformat Parameters
      5. xdget Parameters

  6. Appendixes

    1. Appendix A NCBI Display Formats

      1. Brief Descriptions
      2. Detailed Descriptions and Examples

    2. Appendix B Nucleotide Scoring Schemes

    3. Appendix C NCBI-BLAST Scoring Schemes

      1. NCBI-BLAST Matrices and Gap Costs

    4. Appendix D blast-imager.pl

    5. Appendix E blast2table.pl

  1. Glossary

  2. Colophon

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