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9780596002992

Blast

by ; ;
  • ISBN13:

    9780596002992

  • ISBN10:

    0596002998

  • Format: Paperback
  • Copyright: 2003-07-01
  • Publisher: Oreilly & Associates Inc
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Supplemental Materials

What is included with this book?

Summary

BLAST (Basic Local Alignment Search Tool) is the most important bioinformatics software package available. Used by research biologists, BLAST is a set of similarity search programs that explore all of the available sequence databases for protein or DNA. BLAST will give biologists, computational biology students, and bioinformatics professionals a clear understanding of this program. This incredible book shows them how to get specific answers with BLAST, and how to use the software to interpret the results. Students of computational biology will be able to understand the theory and practice of BLAST, even if they are moving from another field of science. The book is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis.

Author Biography

  1. Ian Korf

    Ian Korf received his B.A. from Cornell University and his Ph.D from Indiana University. His formal training is in molecular biology but he has had a fondness for computer programming since his early teens. His post-doctoral research at Washington University in St. Louis and at The Wellcome Trust Sanger Institute in the U.K. has focused on genomic sequence analysis with an emphasis on comparative genomics and gene prediction. His goal in life is to follow genomes, wherever they happen to take him.
  2. Mark Yandell

    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.
  3. Joseph Bedell

    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.

Table of Contents

Foreword xi
Preface xiii
Part I. Introduction
Hello BLAST
3(16)
What Is BLAST?
3(1)
Using NCBI-BLAST
4(8)
Alternate Output Formats
12(1)
Alternate Alignment Views
13(1)
The Next Step
14(1)
Further Reading
15(4)
Part II. Theory
Biological Sequences
19(21)
The Central Dogma of Molecular Biology
19(8)
Evolution
27(8)
Genomes and Genes
35(3)
Biological Sequences and Similarity
38(1)
Further Reading
39(1)
Sequence Alignment
40(15)
Global Alignment: Needleman-Wunsch
40(6)
Local Alignment: Smith-Waterman
46(4)
Dynamic Programming
50(1)
Algorithmic Complexity
50(1)
Global Versus Local
50(1)
Variations
51(2)
Final Thoughts
53(1)
Further Reading
53(2)
Sequence Similarity
55(20)
Introduction to Information Theory
55(2)
Amino Acid Similarity
57(2)
Scoring Matrices
59(1)
Target Frequencies, lambda, and H
60(4)
Sequence Similarity
64(1)
Karlin-Altschul Statistics
65(2)
Sum Statistics and Sum Scores
67(3)
Further Reading
70(5)
Part III. Practice
BLAST
75(13)
The Five BLAST Programs
75(1)
The BLAST Algorithm
76(11)
Further Reading
87(1)
Anatomy of a BLAST Report
88(8)
Basic Structure
88(2)
Alignments
90(6)
A BLAST Statistics Tutorial
96(20)
Basic BLAST Statistics
96(13)
Using Statistics to Understand BLAST Results
109(1)
Where Did My Oligo Go?
109(7)
20 Tips to Improve Your BLAST Searches
116(14)
Don't Use the Default Parameters
116(1)
Treat BLAST Searches as Scientific Experiments
116(1)
Perform Controls, Especially in the Twilight Zone
117(1)
View BLAST Reports Graphically
118(1)
Use the Karlin-Altschul Equation to Design Experiments
119(1)
When Troubleshooting, Read the Footer First
119(1)
Know When to Use Complexity Filters
120(1)
Mask Repeats in Genomic DNA
121(1)
Segment Large Genomic Sequences
121(2)
Be Skeptical of Hypothetical Proteins
123(1)
Expect Contaminants in EST Databases
123(1)
Use Caution When Searching Raw Sequencing Reads
124(1)
Look for Stop Codons and Frame-Shifts to find Pseudo-Genes
124(1)
Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX
124(2)
Look for Gaps in Coverage as a Sign of Missed Exons
126(1)
Parse BLAST Reports with Bioperl
126(2)
Perform Pilot Experiments
128(1)
Examine Statistical Outliers
128(1)
Use links and topcomboN to Make Sense of Alignment Groups
128(1)
How to Lie with BLAST Statistics
128(2)
BLAST Protocols
130(31)
BLASTN Protocols
131(13)
BLASTP Protocols
144(3)
BLASTX Protocols
147(5)
TBLASTN Protocols
152(3)
TBLASTX Protocols
155(6)
Part IV. Industrial-Strength BLAST
Installation and Command-Line Tutorial
161(27)
NCBI-BLAST Installation
161(5)
WU-BLAST Installation
166(4)
Command-Line Tutorial
170(16)
Editing Scoring Matrices
186(2)
BLAST Databases
188(25)
FASTA Files
188(5)
BLAST Databases
193(5)
Sequence Databases
198(8)
Sequence Database Management Strategies
206(7)
Hardware and Software Optimizations
213(16)
The Persistence of Memory
213(2)
CPUs and Computer Architecture
215(1)
Compute Clusters
216(2)
Distributed Resource Management
218(2)
Software Tricks
220(4)
Optimized NCBI-BLAST
224(5)
Part V. BLAST Reference
NCBI-BLAST Reference
229(38)
Usage Statements
229(1)
Command-Line Syntax
229(1)
blastall Parameters
230(10)
formatdb Parameters
240(2)
fastacmd Parameters
242(3)
megablast Parameters
245(7)
bl2seq Parameters
252(4)
blastpgp Parameters (PSI-BLAST and PHI-BLAST)
256(8)
blastclust Parameters
264(3)
WU-BLAST Reference
267(46)
Usage Statements
268(1)
Command-Line Syntax
268(1)
WU-BLAST Parameters
269(12)
xdformat Parameters
281(4)
xdget Parameters
285(6)
Part VI. Appendixes
A. NCBI Display Formats
291(8)
B. Nucleotide Scoring Schemes
299(3)
C. NCBI-BLAST Scoring Schemes
302(3)
D. blast-imager.pl
305(4)
E. blast2table.pl
309(4)
Glossary 313(6)
Index 319

Supplemental Materials

What is included with this book?

The New copy of this book will include any supplemental materials advertised. Please check the title of the book to determine if it should include any access cards, study guides, lab manuals, CDs, etc.

The Used, Rental and eBook copies of this book are not guaranteed to include any supplemental materials. Typically, only the book itself is included. This is true even if the title states it includes any access cards, study guides, lab manuals, CDs, etc.

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