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Tables of Contents for High Performance Computational Methods for Biological Sequence Analysis
Chapter/Section Title
Page #
Page Count
LIST OF FIGURES
xi
4
LIST OF TABLES
xv
2
PREFACE
xvii
1 INTRODUCTION
1
14
1.1 The Human Genome Project
1
5
1.1.1 Origin
2
1
1.1.2 Goals
3
1
1.1.3 Benefits
4
2
1.2 Informatics
6
6
1.2.1 Data management
6
4
1.2.2 Data analysis
10
2
1.3 Summary
12
3
2 BIOLOGICAL BACKGROUND
15
36
2.1 Introduction
15
2
2.2 Types of biological sequences
17
4
2.3 DNA extraction and amplification
21
11
2.3.1 Preparation
21
4
2.3.2 Amplification
25
7
2.4 Sequencing technology
32
9
2.4.1 Chemical degradation
33
2
2.4.2 Dideoxy chain termination
35
4
2.4.3 Large fragment sequencing strategies
39
1
2.4.4 Large scale sequencing automation
40
1
2.5 Sequence databases
41
7
2.6 Summary
48
3
3 SEQUENCE ANALYSIS ALGORITHMS
51
48
3.1 Introduction
51
1
3.2 Substitution score matrices
52
2
3.2.1 Amino acid substitution matrix
52
2
3.2.2 Nucleic acid substitution matrix
54
1
3.3 Pairwise sequence alignment
54
13
3.3.1 Calculating alignment score
55
7
3.3.2 Constructing alignment
62
5
3.4 Multiple sequence alignment
67
18
3.4.1 Simultaneous alignment
68
2
3.4.2 Clustering strategies
70
8
3.4.3 Randomized strategies
78
7
3.5 Sequence similarity searching
85
11
3.5.1 FASTA
86
3
3.5.2 BLAST
89
2
3.5.3 FLASH
91
5
3.6 Summary
96
3
4 HIGH PERFORMANCE COMPUTING ARCHITECTURES AND TECHNIQUES
99
12
4.1 Introduction
99
1
4.2 Parallelism: what and why?
100
1
4.3 Types of computation
101
2
4.4 Classification schemes
103
3
4.5 Metrics
106
1
4.6 Performance related factors
107
2
4.7 Summary
109
2
5 MULTIPROCESSOR SEQUENCE ALIGNMENT
111
32
5.1 Introduction
111
1
5.2 Pairwise sequence alignment
112
15
5.2.1 Calculating the alignment score
112
7
5.2.2 Constructing the sequence alignment
119
8
5.3 Multiple sequence alignment
127
14
5.3.1 Clustering strategies
127
1
5.3.2 Randomized strategies
128
13
5.4 Summary
141
2
6 MULTIPROCESSOR SEQUENCE SIMILARITY SEARCHING
143
16
6.1 Introduction
143
1
6.2 Fine-grain approach
143
1
6.3 Coarse-grain approach
148
8
6.4 Summary
156
3
7 BIOLOGICAL SEQUENCE RESOURCES ON THE INTERNET
159
32
7.1 Introduction
159
1
7.2 Accessing tools
160
21
7.2.1 Email
160
3
7.2.2 Usenet
163
3
7.2.3 ListServers
166
2
7.2.4 FTP
168
2
7.2.5 Telnet
170
2
7.2.6 Gopher
172
4
7.2.7 World Wide Web
176
5
7.3 Search engines
181
7
7.3.1 Netfind and ph
181
2
7.3.2 Archie
183
2
7.3.3 Veronica
185
1
7.3.4 WWW search engines
186
2
7.4 Summary
188
3
8 LOOKING TO THE FUTURE
191
4
REFERENCES
195
14
INDEX
209