Genome sequencing technology and algorithms:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Boston [u.a.]
Artech House
2008
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XIV, 259 S. graph. Darst. |
| ISBN: | 9781596930940 1596930942 |
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MARC
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Record in the Search Index
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| adam_text | Contents
Parti
The New DNA Sequencing Technology 1
1 An Overview of New DNA Sequencing Technology 3
1.1 An Overview 3
1.1.1 Background 3
1.1.2 Rationale for Technology Development Toward Massively
Parallel Scale DNA Sequencing 4
1.1.3 Goals of Massively Parallel Sequencing Approaches 6
1.2 Massively Parallel Sequencing by Synthesis Pyrosequencing 6
1.2.1 Principle of the Method 6
1.2.2 Pyrosequencing in a Microtiter Plate Format 7
1.2.3 The 454 GS-20 Sequencer 7
1.2.4 Novel Applications Enabled by Massively Parallel
Pyrosequencing 8
1.3 Massively Parallel Sequencing by Other Approaches 8
1.3.1 Sequencing by Synthesis with Reversible Terminators 8
1.3.2 Ligation-Based Sequencing 8
1.3.3 Sequencing by Hybridization 9
vii
viii Genome Sequencing Technology and Algorithms
1.4 Survey of Future Massively Parallel Sequencing Methods 9
1.4.1 Sequencing Within a Zero-Mode Waveguide 9
1.4.2 Nanopore Sequencing Approaches 10
References 11
2 Array-Based Pyrosequencing Technology 15
2.1 Introduction 15
2.2 Pyrosequencing Chemistry 16
2.3 Array-Based Pyrosequencing 17
2.4 454 Sequencing Chemistry 18
2.5 Applications of 454 Sequencing Technology 19
2.5.1 Whole-Genome Sequencing 19
2.5.2 Ultrabroad Sequencing 20
2.5.3 Ultradeep Amplicon Sequencing 20
2.6 Advantages and Challenges 20
2.7 Future of Pyrosequencing 21
References 21
3 The Role of Resequencing Arrays in Revolutionizing
DNA Sequencing 25
3.1 Introduction 25
3.2 DNA Sequencing by Hybridization with Resequencing
Arrays 26
3.3 Resequencing Array Experimental Protocols 28
3.4 Analyzing Resequencing Array Data with ABACUS 29
3.5 Review of RA Applications 33
3.5.1 Human Resequencing 33
3.5.2 Mitochondrial DNA Resequencing 33
3.5-3 Microbial Pathogen Resequencing 35
3.6 Further Challenges 38
References 40
Contents ix
4 Polony Sequencing 43
4.1 Introduction 43
4.2 Overview 44
4.3 Construction of Sequencing Libraries 45
4.4 Template Amplification with Emulsion PCR 46
4.5 Sequencing 48
4.6 Future Directions 49
References 50
5 Genome Sequencing: A Complex Path to Personalized
Medicine K
5.1 Introduction 53
5.2 Personalized Medicine 55
5.3 Heterogeneous Data Sources 56
5.4 Information Modeling 57
5.5 Ontologies and Terminologies 58
5.6 Applications 59
5.7 Conclusion 71
References 72
Part II
Genome Sequencing and Fragment Assembly 77
6 Overview of Genome Assembly Techniques 79
6.1 Genome Sequencing by Shotgun-Sequencing Strategy 79
6.1.1 A Procedure for Whole-Genome Shotgun (WGS)
Sequencing 80
6.2 Trimming Vector and Low-Quality Sequences 82
6.2.1 The Trimming Vector and Low-Quality Sequences
Problem 82
6.3 Fragment Assembly 84
6.3.1 The Fragment Assembly Problem 84
x Genome Sequencing Technology and Algorithms
6.4 Assembly Validation 85
6.4.1 The Assembly Validation Problem 85
6.5 Scaffold Generation 87
6.5.1 The Scaffold Generation Problem 89
6.5.2 Bambus 89
6.5.3 GigAssembler 93
6.6 Finishing 94
6.7 Three Strategies for Whole-Genome Sequencing 94
6.8 Discussion 95
6.8.1 A Thought on an Exploratory Genome Sequencing
Framework 96
Acknowledgments 97
References 97
7 Fragment Assembly Algorithms 101
7.1 TIGR Assembler 102
7.1.1 Merging Fragments with Assemblies 102
7.1.2 Building a Consensus Sequence 102
7.1.3 Handling Repetitive Sequences 103
7.2 Phrap 103
7.3 CAP3 104
7.3.1 Automatics Clipping of 5 and 3 Poor Quality Regions 104
7.3.2 Computation and Evaluation of Overlaps 104
7.3.3 Use of Mate-Pair Constraints in Construction of Contigs 105
7.4 Celera Assembler 105
7.4.1 Kececioglu and Myers Approach 105
7.4.2 The Design Principle of the Celera Whole-Genome
Assembler 107
7.4.3 Overlapper 108
7.4.4 Unitigger 108
7.4.5 Scaffolder 109
7.5 Arachne HO
7.5.1 Contig Assembly 111
Contents xi
7.5.2 Detecting Repeat Contigs and Repeat Supercontigs 111
7.6 EULER 112
7.6.1 Idury-Waterman Algorithm 112
7.6.2 An Overview of EULER 113
7.6.3 Error Correction and Data Corruption 113
7.6.4 Eulerian Superpath 114
7.6.5 Use of Mate-Pair Information 115
7.7 Other Approaches to Fragment Assembly 116
7.7.1 A Genetic Algorithm Approach 116
7.7.2 A Structured Pattern-Matching Approach 117
7.8 Incompleteness of the Survey 119
Acknowledgments 120
References 120
8 Assembly for Double-Ended Short-Read Sequencing
Technologies 123
8.1 Introduction 123
8.2 Short-Read Sequencing Technologies 125
8.3 Assembly for Short-Read Sequencing 128
8.3.1 Algorithmic Methods 129
8.3.2 Simulation Results 129
8.4 Developing a Short-Read-Pair Assembler 132
8.4.1 Analysis 135
References 140
Part III
Beyond Conventional Genome Sequencing 143
9 Genome Characterization in the Post-Human Genome
Project Era 145
9.1 Genome Resequencing and Comparative Assembly 146
9.2 Genotyping Versus Haplotyping 147
9.3 Large-Scale Genome Variations 147
xii Genome Sequencing Technology and Algorithms
9.4 Epigenomics: Genetic Variations Beyond Genome
Sequences 148
9.5 Conclusion 149
References 149
10 The Haplotyping Problem: An Overview of
Computational Models and Solutions 151
10.1 Introduction 151
10.2 Preliminary Definitions 153
10.3 Inferring Haplotypes in a Population 154
10.3.1 The Inference Problem: A General Rule 156
10.3.2 The Pure Parsimony Haplotyping Problem 158
10.3.3 The Inference Problem by the Coalescent Model 158
10.3.4 Xor-Genotyping 161
10.3.5 Incomplete Data 162
10.4 Inferring Haplotypes in Pedigrees 163
10.5 Inferring Haplotypes from Fragments 169
10.6 A Glimpse over Statistical Methods 175
10.7 Discussion 177
Acknowledgments 178
References 178
11 Analysis of Genomic Alterations in Cancer 183
11.1 Introduction 183
11.1.1 Measurement of Copy Number Changes by Array
Hybridization 185
11.1.2 Measurement of Genome Rearrangements by End
Sequence Profiling 187
11.2 Analysis of ESP Data 188
11.3 Combination of Techniques 191
11.4 Future Directions 191
References 192
Contents xiii
12 High-Throughput Assessments of Epigenomics in
Human Disease 197
12.1 Introduction 197
12.2 Epigenetic Phenomena That Regulate Gene Expression 198
12.2.1 Methylation of Deoxycytosine 198
12.2.2 Histone Modifications and Nucleosome Remodeling 198
12.2.3 Small Inhibitory RNA Molecules 199
12.3 Epigenetics and Disease 200
12.3.1 Epigenetics and Developmental and Neurological
Diseases 200
12.3.2 Epigenetics and Cancer 200
12.4 High-Throughput Analyses of Epigenetic Phenomena 201
12.4.1 Gel-Based Approaches 201
12.4.2 Microarrays 212
12.4.3 Cloning/Sequencing 213
12.4.4 Mass Spectrometry 215
12.5 Conclusions 215
Acknowledgments 215
References 216
13 Comparative Sequencing, Assembly, and Anchoring 225
13.1 Comparing an Assembled Genome with Another
Assembled Genome 226
13.2 Mutual Comparison of Genome Fragments 229
13.3 Comparing an Assembled Genome with Genome
Fragments 230
13.3.1 Applications Using Read Anchoring 230
13.3.2 Applications Employing Anchoring of Paired Ends 232
13.3.3 Applications Utilizing Mapping of Clone Reads 233
13.4 Anchoring by Seed-and-Extend Versus Positional
Hashing Methods 234
13.5 The UD-CSD Benchmark for Anchoring 237
xiv Genome Sequencing Technology and Algorithms
13.6 Conclusions 239
References 241
About the Authors 245
Index 251
|
| adam_txt |
Contents
Parti
The New DNA Sequencing Technology 1
1 An Overview of New DNA Sequencing Technology 3
1.1 An Overview 3
1.1.1 Background 3
1.1.2 Rationale for Technology Development Toward Massively
Parallel Scale DNA Sequencing 4
1.1.3 Goals of Massively Parallel Sequencing Approaches 6
1.2 Massively Parallel Sequencing by Synthesis Pyrosequencing 6
1.2.1 Principle of the Method 6
1.2.2 Pyrosequencing in a Microtiter Plate Format 7
1.2.3 The 454 GS-20 Sequencer 7
1.2.4 Novel Applications Enabled by Massively Parallel
Pyrosequencing 8
1.3 Massively Parallel Sequencing by Other Approaches 8
1.3.1 Sequencing by Synthesis with Reversible Terminators 8
1.3.2 Ligation-Based Sequencing 8
1.3.3 Sequencing by Hybridization 9
vii
viii Genome Sequencing Technology and Algorithms
1.4 Survey of Future Massively Parallel Sequencing Methods 9
1.4.1 Sequencing Within a Zero-Mode Waveguide 9
1.4.2 Nanopore Sequencing Approaches 10
References 11
2 Array-Based Pyrosequencing Technology 15
2.1 Introduction 15
2.2 Pyrosequencing Chemistry 16
2.3 Array-Based Pyrosequencing 17
2.4 454 Sequencing Chemistry 18
2.5 Applications of 454 Sequencing Technology 19
2.5.1 Whole-Genome Sequencing 19
2.5.2 Ultrabroad Sequencing 20
2.5.3 Ultradeep Amplicon Sequencing 20
2.6 Advantages and Challenges 20
2.7 Future of Pyrosequencing 21
References 21
3 The Role of Resequencing Arrays in Revolutionizing
DNA Sequencing 25
3.1 Introduction 25
3.2 DNA Sequencing by Hybridization with Resequencing
Arrays 26
3.3 Resequencing Array Experimental Protocols 28
3.4 Analyzing Resequencing Array Data with ABACUS 29
3.5 Review of RA Applications 33
3.5.1 Human Resequencing 33
3.5.2 Mitochondrial DNA Resequencing 33
3.5-3 Microbial Pathogen Resequencing 35
3.6 Further Challenges 38
References 40
Contents ix
4 Polony Sequencing 43
4.1 Introduction 43
4.2 Overview 44
4.3 Construction of Sequencing Libraries 45
4.4 Template Amplification with Emulsion PCR 46
4.5 Sequencing 48
4.6 Future Directions 49
References 50
5 Genome Sequencing: A Complex Path to Personalized
Medicine K
5.1 Introduction 53
5.2 Personalized Medicine 55
5.3 Heterogeneous Data Sources 56
5.4 Information Modeling 57
5.5 Ontologies and Terminologies 58
5.6 Applications 59
5.7 Conclusion 71
References 72
Part II
Genome Sequencing and Fragment Assembly 77
6 Overview of Genome Assembly Techniques 79
6.1 Genome Sequencing by Shotgun-Sequencing Strategy 79
6.1.1 A Procedure for Whole-Genome Shotgun (WGS)
Sequencing 80
6.2 Trimming Vector and Low-Quality Sequences 82
6.2.1 The Trimming Vector and Low-Quality Sequences
Problem 82
6.3 Fragment Assembly 84
6.3.1 The Fragment Assembly Problem 84
x Genome Sequencing Technology and Algorithms
6.4 Assembly Validation 85
6.4.1 The Assembly Validation Problem 85
6.5 Scaffold Generation 87
6.5.1 The Scaffold Generation Problem 89
6.5.2 Bambus 89
6.5.3 GigAssembler 93
6.6 Finishing 94
6.7 Three Strategies for Whole-Genome Sequencing 94
6.8 Discussion 95
6.8.1 A Thought on an Exploratory Genome Sequencing
Framework 96
Acknowledgments 97
References 97
7 Fragment Assembly Algorithms 101
7.1 TIGR Assembler 102
7.1.1 Merging Fragments with Assemblies 102
7.1.2 Building a Consensus Sequence 102
7.1.3 Handling Repetitive Sequences 103
7.2 Phrap 103
7.3 CAP3 104
7.3.1 Automatics Clipping of 5'and 3'Poor Quality Regions 104
7.3.2 Computation and Evaluation of Overlaps 104
7.3.3 Use of Mate-Pair Constraints in Construction of Contigs 105
7.4 Celera Assembler 105
7.4.1 Kececioglu and Myers Approach 105
7.4.2 The Design Principle of the Celera Whole-Genome
Assembler 107
7.4.3 Overlapper 108
7.4.4 Unitigger 108
7.4.5 Scaffolder 109
7.5 Arachne HO
7.5.1 Contig Assembly 111
Contents xi
7.5.2 Detecting Repeat Contigs and Repeat Supercontigs 111
7.6 EULER 112
7.6.1 Idury-Waterman Algorithm 112
7.6.2 An Overview of EULER 113
7.6.3 Error Correction and Data Corruption 113
7.6.4 Eulerian Superpath 114
7.6.5 Use of Mate-Pair Information 115
7.7 Other Approaches to Fragment Assembly 116
7.7.1 A Genetic Algorithm Approach 116
7.7.2 A Structured Pattern-Matching Approach 117
7.8 Incompleteness of the Survey 119
Acknowledgments 120
References 120
8 Assembly for Double-Ended Short-Read Sequencing
Technologies 123
8.1 Introduction 123
8.2 Short-Read Sequencing Technologies 125
8.3 Assembly for Short-Read Sequencing 128
8.3.1 Algorithmic Methods 129
8.3.2 Simulation Results 129
8.4 Developing a Short-Read-Pair Assembler 132
8.4.1 Analysis 135
References 140
Part III
Beyond Conventional Genome Sequencing 143
9 Genome Characterization in the Post-Human Genome
Project Era 145
9.1 Genome Resequencing and Comparative Assembly 146
9.2 Genotyping Versus Haplotyping 147
9.3 Large-Scale Genome Variations 147
xii Genome Sequencing Technology and Algorithms
9.4 Epigenomics: Genetic Variations Beyond Genome
Sequences 148
9.5 Conclusion 149
References 149
10 The Haplotyping Problem: An Overview of
Computational Models and Solutions 151
10.1 Introduction 151
10.2 Preliminary Definitions 153
10.3 Inferring Haplotypes in a Population 154
10.3.1 The Inference Problem: A General Rule 156
10.3.2 The Pure Parsimony Haplotyping Problem 158
10.3.3 The Inference Problem by the Coalescent Model 158
10.3.4 Xor-Genotyping 161
10.3.5 Incomplete Data 162
10.4 Inferring Haplotypes in Pedigrees 163
10.5 Inferring Haplotypes from Fragments 169
10.6 A Glimpse over Statistical Methods 175
10.7 Discussion 177
Acknowledgments 178
References 178
11 Analysis of Genomic Alterations in Cancer 183
11.1 Introduction 183
11.1.1 Measurement of Copy Number Changes by Array
Hybridization 185
11.1.2 Measurement of Genome Rearrangements by End
Sequence Profiling 187
11.2 Analysis of ESP Data 188
11.3 Combination of Techniques 191
11.4 Future Directions 191
References 192
Contents xiii
12 High-Throughput Assessments of Epigenomics in
Human Disease 197
12.1 Introduction 197
12.2 Epigenetic Phenomena That Regulate Gene Expression 198
12.2.1 Methylation of Deoxycytosine 198
12.2.2 Histone Modifications and Nucleosome Remodeling 198
12.2.3 Small Inhibitory RNA Molecules 199
12.3 Epigenetics and Disease 200
12.3.1 Epigenetics and Developmental and Neurological
Diseases 200
12.3.2 Epigenetics and Cancer 200
12.4 High-Throughput Analyses of Epigenetic Phenomena 201
12.4.1 Gel-Based Approaches 201
12.4.2 Microarrays 212
12.4.3 Cloning/Sequencing 213
12.4.4 Mass Spectrometry 215
12.5 Conclusions 215
Acknowledgments 215
References 216
13 Comparative Sequencing, Assembly, and Anchoring 225
13.1 Comparing an Assembled Genome with Another
Assembled Genome 226
13.2 Mutual Comparison of Genome Fragments 229
13.3 Comparing an Assembled Genome with Genome
Fragments 230
13.3.1 Applications Using Read Anchoring 230
13.3.2 Applications Employing Anchoring of Paired Ends 232
13.3.3 Applications Utilizing Mapping of Clone Reads 233
13.4 Anchoring by Seed-and-Extend Versus Positional
Hashing Methods 234
13.5 The UD-CSD Benchmark for Anchoring 237
xiv Genome Sequencing Technology and Algorithms
13.6 Conclusions 239
References 241
About the Authors 245
Index 251 |
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| publisher | Artech House |
| record_format | marc |
| spelling | Genome sequencing technology and algorithms Sun Kim, ... ed. Boston [u.a.] Artech House 2008 XIV, 259 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Genomes Analysis Nucleotide sequence Sequenzanalyse Chemie (DE-588)4132277-0 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Genanalyse (DE-588)4200230-8 s Sequenzanalyse Chemie (DE-588)4132277-0 s b DE-604 Kim, Sun Sonstige oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016413612&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Genome sequencing technology and algorithms Genomes Analysis Nucleotide sequence Sequenzanalyse Chemie (DE-588)4132277-0 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4132277-0 (DE-588)4200230-8 (DE-588)4143413-4 |
| title | Genome sequencing technology and algorithms |
| title_auth | Genome sequencing technology and algorithms |
| title_exact_search | Genome sequencing technology and algorithms |
| title_exact_search_txtP | Genome sequencing technology and algorithms |
| title_full | Genome sequencing technology and algorithms Sun Kim, ... ed. |
| title_fullStr | Genome sequencing technology and algorithms Sun Kim, ... ed. |
| title_full_unstemmed | Genome sequencing technology and algorithms Sun Kim, ... ed. |
| title_short | Genome sequencing technology and algorithms |
| title_sort | genome sequencing technology and algorithms |
| topic | Genomes Analysis Nucleotide sequence Sequenzanalyse Chemie (DE-588)4132277-0 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Genomes Analysis Nucleotide sequence Sequenzanalyse Chemie Genanalyse Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016413612&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT kimsun genomesequencingtechnologyandalgorithms |