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BLAST
By Joseph Bedell, Ian Korf, Mark Yandell
 
Publisher: O'Reilly
Pub Date: July 2003
ISBN: 0-596-00299-8
Pages: 360


   Copyright
   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
    Part I:  Introduction
      Chapter 1.  Hello BLAST
      Section 1.1.  What Is BLAST?
      Section 1.2.  Using NCBI-BLAST
      Section 1.3.  Alternate Output Formats
      Section 1.4.  Alternate Alignment Views
      Section 1.5.  The Next Step
      Section 1.6.  Further Reading
    Part II:  Theory
      Chapter 2.  Biological Sequences
      Section 2.1.  The Central Dogma of Molecular Biology
      Section 2.2.  Evolution
      Section 2.3.  Genomes and Genes
      Section 2.4.  Biological Sequences and Similarity
      Section 2.5.  Further Reading
      Chapter 3.  Sequence Alignment
      Section 3.1.  Global Alignment: Needleman-Wunsch
      Section 3.2.  Local Alignment: Smith-Waterman
      Section 3.3.  Dynamic Programming
      Section 3.4.  Algorithmic Complexity
      Section 3.5.  Global Versus Local
      Section 3.6.  Variations
      Section 3.7.  Final Thoughts
      Section 3.8.  Further Reading
      Chapter 4.  Sequence Similarity
      Section 4.1.  Introduction to Information Theory
      Section 4.2.  Amino Acid Similarity
      Section 4.3.  Scoring Matrices
      Section 4.4.  Target Frequencies, lambda, and H
      Section 4.5.  Sequence Similarity
      Section 4.6.  Karlin-Altschul Statistics
      Section 4.7.  Sum Statistics and Sum Scores
      Section 4.8.  Further Reading
    Part III:  Practice
      Chapter 5.  BLAST
      Section 5.1.  The Five BLAST Programs
      Section 5.2.  The BLAST Algorithm
      Section 5.3.  Further Reading
      Chapter 6.  Anatomy of a BLAST Report
      Section 6.1.  Basic Structure
      Section 6.2.  Alignments
      Chapter 7.  A BLAST Statistics Tutorial
      Section 7.1.  Basic BLAST Statistics
      Section 7.2.  Using Statistics to Understand BLAST Results
      Section 7.3.  Where Did My Oligo Go?
      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
      Chapter 9.  BLAST Protocols
      Section 9.1.  BLASTN Protocols
      Section 9.2.  BLASTP Protocols
      Section 9.3.  BLASTX Protocols
      Section 9.4.  TBLASTN Protocols
      Section 9.5.  TBLASTX Protocols
    Part IV:  Industrial-Strength BLAST
      Chapter 10.  Installation and Command-Line Tutorial
      Section 10.1.  NCBI-BLAST Installation
      Section 10.2.  WU-BLAST Installation
      Section 10.3.  Command-Line Tutorial
      Section 10.4.  Editing Scoring Matrices
      Chapter 11.  BLAST Databases
      Section 11.1.  FASTA Files
      Section 11.2.  BLAST Databases
      Section 11.3.  Sequence Databases
      Section 11.4.  Sequence Database Management Strategies
      Chapter 12.  Hardware and Software Optimizations
      Section 12.1.  The Persistence of Memory
      Section 12.2.  CPUs and Computer Architecture
      Section 12.3.  Compute Clusters
      Section 12.4.  Distributed Resource Management
      Section 12.5.  Software Tricks
      Section 12.6.  Optimized NCBI-BLAST
    Part V:  BLAST Reference
      Chapter 13.  NCBI-BLAST Reference
      Section 13.1.  Usage Statements
      Section 13.2.  Command-Line Syntax
      Section 13.3.  blastall Parameters
      Section 13.4.  formatdb Parameters
      Section 13.5.  fastacmd Parameters
      Section 13.6.  megablast Parameters
      Section 13.7.  bl2seq Parameters
      Section 13.8.  blastpgp Parameters (PSI-BLAST and PHI-BLAST)
      Section 13.9.  blastclust Parameters
      Chapter 14.  WU-BLAST Reference
      Section 14.1.  Usage Statements
      Section 14.2.  Command-Line Syntax
      Section 14.3.  WU-BLAST Parameters
      Section 14.4.  xdformat Parameters
      Section 14.5.  xdget Parameters
    Part VI:  Appendixes
      Appendix A.  NCBI Display Formats
      Section A.1.  Brief Descriptions
      Section A.2.  Detailed Descriptions and Examples
      Appendix B.  Nucleotide Scoring Schemes
      Appendix C.  NCBI-BLAST Scoring Schemes
      Section C.1.  NCBI-BLAST Matrices and Gap Costs
      Appendix D.  blast-imager.pl
      Appendix E.  blast2table.pl
   Glossary
      Numbers
      A-G
      H-U
   Colophon
   Index
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