Guide to Human Genome Computing
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Table of contents
- Contentsv
- Contributorsix
- Prefacexiii
- Chapter 1. Introduction to Human Genome Computing Via the World Wide Web1
- 1 Introduction1
- 2 Equipment for the tour2
- 3 Genome databases3
- 4 Analytic tools24
- 5 Conclusion38
- 6 URLs39
- Chapter 2. Biological Materials and Services41
- 1 Introduction41
- 2 Genomic resources available42
- 3 Chromosome-specific libraries46
- 4 CpG island libraries46
- 5 cDNA libraries47
- 6 Probe and primer banks47
- 7 Cell lines48
- 8 Cell hybrid panels48
- 9 Backcross panels48
- Chapter 3. Managing Pedigree and Genotype Data49
- 1 Introduction49
- 2 Fundamentals50
- 3 Modelling the domain55
- 4 Implementing the database59
- 5 Interfacing with analysis programs64
- 6 Displaying and managing data73
- 7 Further development73
- Chapter 4. Linkage Analysis Using Affected Sib-Pairs75
- 1 Introduction75
- 2 Genetic identity-by-descent between sib-pairs75
- 3 Genetic identity-by-descent and recombination fraction77
- 4 Identity-by-descent distribution for an affected sib-pair78
- 5 Methods of affected sib-pair analysis81
- 6 Affected sib-pair analysis: strengths and limitations84
- 7 Conclusion85
- List of computer programs87
- Chapter 5. Comparative Mapping in Humans and Vertebrates89
- 1 Conservation of genes89
- 2 Conservation of linkage groups92
- 3 Value of comparative mapping94
- 4 Single-species databases95
- 5 Protein families107
- 6 Comparative mapping databases109
- Chapter 6. Radiation Hybrid Mapping113
- 1 Introduction113
- 2 Background114
- 3 RH mapping concepts115
- 4 Radiation hybrid mapping programs119
- 5 Conclusions145
- Chapter 7. Sequence Ready Clone Maps151
- 1 Introduction151
- 2 Strategy153
- 3 Software for sequence ready maps155
- 4 Long-range map construction (SAM, Z-RHMAPPER)156
- 5 STS-content data storage using ACEDB159
- 6 Sequence ready contig construction using FPC160
- 7 Process tracking and coordination172
- 8 Conclusions177
- Chapter 8. Software for Human Genome Sequencing181
- 1 Introduction181
- 2 Overview182
- 3 Gel image processing182
- 4 Sequence preprocessing185
- 5 Sequence assembly189
- 6 Editing and finishing192
- 7 Feature identification197
- 8 Quality control200
- 9 The finished sequence200
- 10 Conclusion201
- 11 Finding software on the Web202
- Chapter 9. Human EST Sequences205
- 1 Introduction205
- 2 Background205
- 3 Generation of the EST data206
- 4 Reasons for EST sequencing207
- 5 Publicly available EST data209
- 6 EST analysis tools211
- 7 Biological resources212
- 8 WWW resources for ESTs213
- 9 Summary213
- Chapter 10. Prediction of Human Gene Structure215
- 1 Introduction215
- 2 Genome structure216
- 3 Approaches to evaluate prediction accuracy217
- 4 Functional sites in nucleotide sequences219
- 5 Functional regions in nucleotide sequences230
- 6 Protein coding gene structure prediction236
- 7 Analysis of potential proteins coded by predicted genes251
- 8 RNA-coding gene structure prediction252
- 9 Sequence analysis252
- Chapter 11. Gene Finding: Putting the Parts Together261
- 1 Introduction261
- 2 Dynamic programming262
- 3 State models266
- 4 Performance comparison271
- 5 Conclusion272
- Chapter 12. Gene-Expression Databases275
- 1 Introduction275
- 2 The scope of gene-expression databases277
- 3 A survey of gene-expression data278
- 4 A survey of gene-expression databases284
- 5 The future of gene-expression databases292
- Index295
The Guide to Human Genome Computing is invaluable to scientists who wish to make use of the powerful computing tools now available to assist them in the field of human genome analysis. This book clearly explains access and use of sequence databases, and presents the various computer packages used to analyze DNA sequences, measure linkage analysis, compare and align DNA sequences from different genes or organisms, and infer structural and functional information about proteins from sequence data.
This Second Edition contains completely updated material. Rather than a revision of the previous volume, the Second Edition is essentially a new book, based on the subjects which will be of interest over the coming years. This new book is international, both in scope and authorship.
Computing resources for the following are clearly explained:
* Internet resources - databases etc.
* Genetic analysis
* Sib-pair studies
* Comparative mapping
* Radiation hybrids
* Sequence ready clone maps
* Human genome sequencing
* ESTs
* Gene prediction
* Gene expression
This Second Edition contains completely updated material. Rather than a revision of the previous volume, the Second Edition is essentially a new book, based on the subjects which will be of interest over the coming years. This new book is international, both in scope and authorship.
Computing resources for the following are clearly explained:
* Internet resources - databases etc.
* Genetic analysis
* Sib-pair studies
* Comparative mapping
* Radiation hybrids
* Sequence ready clone maps
* Human genome sequencing
* ESTs
* Gene prediction
* Gene expression