BLAST / by Ian Korf, Mark Yandell and Joseph Bedell ; [foreword by Stephen Altschul].

Format:

Book

Author/Creator:

Korf, Ian.

Contributor:

Yandell, Mark.

Bedell, Joseph.

Language:

English

Subjects (All):

BLAST (Computer file).

Biology--Data processing.

Biology.

Amino acid sequence--Databases.

Amino acid sequence.

Nucleotide sequence--Databases.

Nucleotide sequence.

Database searching.

Databases.

Physical Description:

xviii, 339 pages : illustrations ; 24 cm

Edition:

First edition.

Other Title:

Basic Local Alignment Search Tool

Place of Publication:

Sebastopol, CA : O'Reilly & Associates, 2003.

Summary:

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 bioinformaties. 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 bioinformaties 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 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. BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis.

Contents:

Using NCBI-BLAST 4

Alternate Output Formats 12

Alternate Alignment Views 13

Part II. Theory

2. Biological Sequences 19

The Central Dogma of Molecular Biology 19

Evolution 27

Genomes and Genes 35

Biological Sequences and Similarity 38

3. Sequence Alignment 40

Global Alignment: Needleman-Wunsch 40

Local Alignment: Smith-Waterman 46

Dynamic Programming 50

Algorithmic Complexity 50

Global Versus Local 50

Variations 51

4. Sequence Similarity 55

Introduction to Information Theory 55

Amino Acid Similarity 57

Scoring Matrices 59

Target Frequencies, lambda, and H 60

Sequence Similarity 64

Karlin-Altschul Statistics 65

Sum Statistics and Sum Scores 67

Part III. Practice

5. BLAST 75

The Five BLAST Programs 75

The BLAST Algorithm 76

6. Anatomy of a BLAST Report 88

Basic Structure 88

Alignments 90

7. A BLAST Statistics Tutorial 96

Basic BLAST Statistics 96

Using Statistics to Understand BLAST Results 109

Where Did My Oligo Go? 109

8. 20 Tips to Improve Your BLAST Searches 116

8.1 Don't Use the Default Parameters 116

8.2 Treat BLAST Searches as Scientific Experiments 116

8.3 Perform Controls, Especially in the Twilight Zone 117

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 130

BLASTN Protocols 131

BLASTP Protocols 144

BLASTX Protocols 147

TBLASTN Protocols 152

TBLASTX Protocols 155

Part IV. Industrial-Strength BLAST

10. Installation and Command-Line Tutorial 161

NCBI-BLAST Installation 161

WU-BLAST Installation 166

Command-Line Tutorial 170

Editing Scoring Matrices 186

11. BLAST Databases 188

FASTA Files 188

BLAST Databases 193

Sequence Databases 198

Sequence Database Management Strategies 206

12. Hardware and Software Optimizations 213

The Persistence of Memory 213

CPUs and Computer Architecture 215

Compute Clusters 216

Distributed Resource Management 218

Software Tricks 220

Optimized NCBI-BLAST 224

Part V. BLAST Reference

13. NCBI-BLAST Reference 229

Usage Statements 229

Command-Line Syntax 229

blastall Parameters 230

formatdb Parameters 240

fastacmd Parameters 242

megablast Parameters 245

bl2seq Parameters 252

blastpgp Parameters (PSI-BLAST and PHI-BLAST) 256

blastclust Parameters 264

14. WU-BLAST Reference 267

Usage Statements 268

Command-Line Syntax 268

WU-BLAST Parameters 269

xdformat Parameters 281

xdget Parameters 285

A. NCBI Display Formats 291

B. Nucleotide Scoring Schemes 299

C. NCBI-BLAST Scoring Schemes 302

D. blast-imager.pl 305

E. blast2table.pl 309.

Notes:

"An essential guide to the Basic Local Alignment Search Tool"--Cover.

Includes bibliographical references and index.

ISBN:

0596002998

OCLC:

51738695