BLAST
Paperback Engels 2003 9780596002992Samenvatting
Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. 'BLAST' (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power.
'BLAST' is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs.
Some of the topics covered include:
- BLAST basics and the NCBI web interface
- How to select appropriate search parameters
- BLAST programs: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, PHI-BLAST, and PSI BLAST
- Detailed BLAST references, including NCBI-BLAST and WU-BLAST
- Understanding biological sequences
- Sequence similarity, homology, scoring matrices, scores, and evolution
- Sequence Alignment
- Calculating BLAST statistics
- Industrial-strength BLAST, including developing applications with Perl and BLAST
BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. This is a book that any biologist should own
Specificaties
Lezersrecensies
Inhoudsopgave
Preface
Part I. Introduction
1. Hello BLAST
What Is BLAST?
Using NCBI-BLAST
Alternate Output Formats
Alternate Alignment Views
The Next Step
Further Reading
Part II. Theory
2. Biological Sequences
The Central Dogma of Molecular Biology
Evolution
Genomes and Genes
Biological Sequences and Similarity
Further Reading
3. Sequence Alignment
Global Alignment: Needleman-Wunsch
Local Alignment: Smith-Waterman
Dynamic Programming
Algorithmic Complexity
Global Versus Local
Variations
Final Thoughts
Further Reading
4. Sequence Similarity
Introduction to Information Theory
Amino Acid Similarity
Scoring Matrices
Target Frequencies, lambda, and H
Sequence Similarity
Karlin-Altschul Statistics
Sum Statistics and Sum Scores
Further Reading
Part III. Practice
5. BLAST
The Five BLAST Programs
The BLAST Algorithm
Further Reading
6. Anatomy of a BLAST Report
Basic Structure
Alignments
7. A BLAST Statistics Tutorial
Basic BLAST Statistics
Using Statistics to Understand BLAST Results
Where Did My Oligo Go?
8. 20 Tips to Improve Your BLAST Searches
8.1 Don't Use the Default Parameters 116
8.2 Treat BLAST Searches as Scientific Experiments 116
8.4 View BLAST Reports Graphically 118
8.5 Use the Karlin-Altschul Equation to Design Experiments 119
8.6 When Troubleshooting, Read the Footer First 119
8.7 Know When to Use Complexity Filters 120
8.8 Mask Repeats in Genomic DNA 121
8.9 Segment Large Genomic Sequences 121
8.10 Be Skeptical of Hypothetical Proteins 123
8.11 Expect Contaminants in EST Databases 123
8.12 Use Caution When Searching Raw Sequencing Reads 124
8.13 Look for Stop Codons and Frame-Shifts to find Pseudo-Genes 124
8.14 Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX 124
8.15 Look for Gaps in Coverage as a Sign of Missed Exons 126
8.16 Parse BLAST Reports with Bioperl 126
8.17 Perform Pilot Experiments 128
8.18 Examine Statistical Outliers 128
8.19 Use links and topcomboN to Make Sense of Alignment Groups 128
8.20 How to Lie with BLAST Statistics 128
9. BLAST Protocols
BLASTN Protocols
BLASTP Protocols
BLASTX Protocols
TBLASTN Protocols
TBLASTX Protocols
Part IV. Industrial-Strength BLAST
10. Installation and Command-Line Tutorial
NCBI-BLAST Installation
WU-BLAST Installation
Command-Line Tutorial
Editing Scoring Matrices
11. BLAST Databases
FASTA Files
BLAST Databases
Sequence Databases
Sequence Database Management Strategies
12. Hardware and Software Optimizations
The Persistence of Memory
CPUs and Computer Architecture
Compute Clusters
Distributed Resource Management
Software Tricks
Optimized NCBI-BLAST
Part V. BLAST Reference
13. NCBI-BLAST Reference
Usage Statements
Command-Line Syntax
blastall Parameters
formatdb Parameters
fastacmd Parameters
megablast Parameters
bl2seq Parameters
blastpgp Parameters (PSI-BLAST and PHI-BLAST)
blastclust Parameters
14. WU-BLAST Reference
Usage Statements
Command-Line Syntax
WU-BLAST Parameters
xdformat Parameters
xdget Parameters
Part VI. Appendixes
A. NCBI Display Formats
B. Nucleotide Scoring Schemes
C. NCBI-BLAST Scoring Schemes
D. blast-imager.pl
E. blast2table.pl
Glossary
Index
Rubrieken
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