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Blast An Essential Guide to the Basic Local Alignment Search Tool

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ISBN-10: 0596002998

ISBN-13: 9780596002992

Edition: 2003

Authors: Ian Korf, Mark Yandell, Joseph Bedell

List price: $49.99
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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…    
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Book details

List price: $49.99
Copyright year: 2003
Publisher: O'Reilly Media, Incorporated
Publication date: 8/19/2003
Binding: Paperback
Pages: 362
Size: 6.75" wide x 9.00" long x 0.75" tall
Weight: 1.298
Language: English

Mark Yandell received his PhD in Molecular, Cellular and Developmental Biology from the University of Colorado, Boulder. After graduation, he joined the Genome Sequencing Center at Washington University, where he pursued post-doctoral studies in computational biology, genome annotation and SNP discovery. In 1999 he joined Celera Genomics, where he wrote much of the software used by Celera to annotate and analyze the drosophila, human, mouse and mosquito genomes. He recently joined the Berkeley Drosophila Genome Project.

Joseph Bedell received his B.S. in Genetics from the University of Georgia in 1991 then worked on mosquito genetics at the Centers for Disease Control and Prevention in Atlanta. He went on to complete a Ph.D. in human genetics at the University of California, Irvine in 1999. Joseph, like his co-authors, completed a post-doc in mammalian gene annotation with Warren Gish, one of the original developers of BLAST. He is currently the Director of Bioinformatics for Orion Genomics in St. Louis where he spends his days (and nights) using BLAST to answer important biological and phylogenetic questions in plants.

Foreword
Preface
Introduction
Hello BLAST
What Is BLAST?
Using NCBI-BLAST
Alternate Output Formats
Alternate Alignment Views
The Next Step
Further Reading
Theory
Biological Sequences
The Central Dogma of Molecular Biology
Evolution
Genomes and Genes
Biological Sequences and Similarity
Further Reading
Sequence Alignment
Global Alignment: Needleman-Wunsch
Local Alignment: Smith-Waterman
Dynamic Programming
Algorithmic Complexity
Global Versus Local
Variations
Final Thoughts
Further Reading
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
Practice
BLAST
The Five BLAST Programs
The BLAST Algorithm
Further Reading
Anatomy of a BLAST Report
Basic Structure
Alignments
A BLAST Statistics Tutorial
Basic BLAST Statistics
Using Statistics to Understand BLAST Results
Where Did My Oligo Go?
20 Tips to Improve Your BLAST Searches
Don't Use the Default Parameters
Treat BLAST Searches as Scientific Experiments
Perform Controls, Especially in the Twilight Zone
View BLAST Reports Graphically
Use the Karlin-Altschul Equation to Design Experiments
When Troubleshooting, Read the Footer First
Know When to Use Complexity Filters
Mask Repeats in Genomic DNA
Segment Large Genomic Sequences
Be Skeptical of Hypothetical Proteins
Expect Contaminants in EST Databases
Use Caution When Searching Raw Sequencing Reads
Look for Stop Codons and Frame-Shifts to find Pseudo-Genes
Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX
Look for Gaps in Coverage as a Sign of Missed Exons
Parse BLAST Reports with Bioperl
Perform Pilot Experiments
Examine Statistical Outliers
Use links and topcomboN to Make Sense of Alignment Groups
How to Lie with BLAST Statistics
BLAST Protocols
BLASTN Protocols
BLASTP Protocols
BLASTX Protocols
TBLASTN Protocols
TBLASTX Protocols
Industrial-Strength BLAST
Installation and Command-Line Tutorial
NCBI-BLAST Installation
WU-BLAST Installation
Command-Line Tutorial
Editing Scoring Matrices
BLAST Databases
FASTA Files
BLAST Databases
Sequence Databases
Sequence Database Management Strategies
Hardware and Software Optimizations
The Persistence of Memory
CPUs and Computer Architecture
Compute Clusters
Distributed Resource Management
Software Tricks
Optimized NCBI-BLAST
BLAST Reference
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
WU-BLAST Reference
Usage Statements
Command-Line Syntax
WU-BLAST Parameters
xdformat Parameters
xdget Parameters
Appendixes
NCBI Display Formats
Nucleotide Scoring Schemes
NCBI-BLAST Scoring Schemes
blast-imager.pl
blast2table.pl
Glossary
Index