Genome Sequencing Technology and Algorithms

Genome Sequencing Technolog and Algorithms......Page 1
List of Contributors......Page 5
Contents......Page 7
Part I The New DNA Sequencing Technology......Page 15
1.1 An Overview......Page 17
1.2 Massively Parallel Sequencing by Synthesis Pyrosequencing......Page 20
1.3 Massively Parallel Sequencing by Other Approaches......Page 22
1.4 Survey of Future Massively Parallel Sequencing Methods......Page 23
2.1 Introduction......Page 29
2.2 Pyrosequencing Chemistry......Page 30
2.3 Array-Based Pyrosequencing......Page 31
2.4 454 Sequencing Chemistry......Page 32
2.5 Applications of 454 Sequencing Technology......Page 33
2.6 Advantages and Challenges......Page 34
2.7 Future of Pyrosequencing......Page 35
3.1 Introduction......Page 39
3.2 DNA Sequencing by Hybridization with ResequencingArrays......Page 40
3.3 Resequencing Array Experimental Protocols......Page 42
3.4 Analyzing Resequencing Array Data with ABACUS......Page 43
3.5 Review of RA Applications......Page 47
3.6 Further Challenges......Page 52
4.1 Introduction......Page 57
4.2 Overview......Page 58
4.3 Construction of Sequencing Libraries......Page 59
4.4 Template Amplification with Emulsion PCR......Page 60
4.5 Sequencing......Page 62
4.6 Future Directions......Page 63
5.1 Introduction......Page 67
5.2 Personalized Medicine......Page 69
5.3 Heterogeneous Data Sources......Page 70
5.4 Information Modeling......Page 71
5.5 Ontologies and Terminologies......Page 72
5.6 Applications......Page 73
5.7 Conclusion......Page 85
Part II Genome Sequencing and Fragment Assembly......Page 91
6.1 Genome Sequencing by Shotgun-Sequencing Strategy......Page 93
6.2 Trimming Vector and Low-Quality Sequences......Page 96
6.3 Fragment Assembly......Page 98
6.4 Assembly Validation......Page 99
6.5 Scaffold Generation......Page 101
6.7 Three Strategies for Whole-Genome Sequencing......Page 108
6.8 Discussion......Page 109
7 Fragment Assembly Algorithms......Page 115
7.1 TIGR Assembler......Page 116
7.2 Phrap......Page 117
7.3 CAP3......Page 118
7.4 Celera Assembler......Page 119
7.5 Arachne......Page 124
7.6 EULER......Page 126
7.7 Other Approaches to Fragment Assembly......Page 131
7.8 Incompleteness of the Survey......Page 133
8.1 Introduction......Page 137
8.2 Short-Read Sequencing Technologies......Page 139
8.3 Assembly for Short-Read Sequencing......Page 142
8.4 Developing a Short-Read-Pair Assembler......Page 146
Part III Beyond Conventional Genome Sequencing......Page 157
9 Genome Characterization in the Post–Human GenomeProject Era......Page 159
9.1 Genome Resequencing and Comparative Assembly......Page 160
9.3 Large-Scale Genome Variations......Page 161
9.4 Epigenomics: Genetic Variations Beyond GenomeSequences......Page 162
9.5 Conclusion......Page 163
10.1 Introduction......Page 165
10.2 Preliminary Definitions......Page 167
10.3 Inferring Haplotypes in a Population......Page 168
10.4 Inferring Haplotypes in Pedigrees......Page 177
10.5 Inferring Haplotypes from Fragments......Page 183
10.6 A Glimpse over Statistical Methods......Page 189
10.7 Discussion......Page 191
11.1 Introduction......Page 197
11.2 Analysis of ESP Data......Page 202
11.4 Future Directions......Page 205
12.1 Introduction......Page 211
12.2 Epigenetic Phenomena That Regulate Gene Expression......Page 212
12.3 Epigenetics and Disease......Page 214
12.4 High-Throughput Analyses of Epigenetic Phenomena......Page 215
12.5 Conclusions......Page 229
13 Comparative Sequencing, Assembly, and Anchoring......Page 239
13.1 Comparing an Assembled Genome with AnotherAssembled Genome......Page 240
13.2 Mutual Comparison of Genome Fragments......Page 243
13.3 Comparing an Assembled Genome with GenomeFragments......Page 244
13.4 Anchoring by Seed-and-Extend Versus PositionalHashing Methods......Page 248
13.5 The UD-CSD Benchmark for Anchoring......Page 251
13.6 Conclusions......Page 253
About the Authors......Page 259
Index......Page 265