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Tables of Contents for Blast
Chapter/Section Title
Page #
Page Count
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