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Tables of Contents for Guide to Human Genome Computing
Chapter/Section Title
Page #
Page Count
Contributors
ix
4
Preface
xiii
 
1 Introduction to Human Genome Computing Via the World Wide Web
1
40
Lincoln D. Stein
1 Introduction
1
1
2 Equipment for the tour
2
1
3 Genome databases
3
21
4 Analytic tools
24
14
5 Conclusion
38
1
6 URLs
39
2
2 Biological Materials and Services
41
8
Michael Rhodes
Ramnath Elaswarapu
1 Introduction
41
1
2 Genomic resources available
42
4
3 Chromosome-specific libraries
46
1
4 CpG island libraries
46
1
5 cDNA libraries
47
1
6 Probe and primer banks
47
1
7 Cell lines
48
1
8 Cell hybrid panels
48
1
9 Backcross panels
48
1
3 Managing Pedigree and Genotype Data
49
26
Stephen P. Bryant
1 Introduction
49
1
2 Fundamentals
50
5
3 Modelling the domain
55
4
4 Implementing the database
59
5
5 Interfacing with analysis programs
64
9
6 Displaying and managing data
73
1
7 Further development
73
2
4 Linkage Analysis Using Affected Sib-Pairs
75
14
Pak Sham
Jinghua Zhao
1 Introduction
75
1
2 Genetic identity-by-descent between sib-pairs
75
2
3 Genetic identity-by-descent and recombination fraction
77
1
4 Identity-by-descent distribution for an affected sib-pair
78
3
5 Methods of affected sib-pair analysis
81
3
6 Affected sib-pair analysis: strengths and limitations
84
1
7 Conclusion
85
2
List of computer programs
87
2
5 Comparative Mapping in Humans and Vertebrates
89
24
Martin Bishop
1 Conservation of genes
89
3
2 Conservation of linkage groups
92
2
3 Value of comparative mapping
94
1
4 Single-species databases
95
12
5 Protein families
107
2
6 Comparative mapping databases
109
4
6 Radiation Hybrid Mapping
113
38
Linda McCarthy
Carol Soderlund
1 Introduction
113
1
2 Background
114
1
3 RH mapping concepts
115
4
4 Radiation hybrid mapping programs
119
26
5 Conclusions
145
6
7 Sequence Ready Clone Maps
151
30
Carol Soderlund
Simon Gregory
Ian Dunham
1 Introduction
151
2
2 Strategy
153
2
3 Software for sequence ready maps
155
1
4 Long-range map construction (SAM, Z-RHMAPPER)
156
3
5 STS-content data storage using ACEDB
159
1
6 Sequence ready contig construction using FPC
160
12
7 Process tracking and coordination
172
5
8 Conclusions
177
4
8 Software for Human Genome Sequencing
181
24
Simon Dear
1 Introduction
181
1
2 Overview
182
1
3 Gel image processing
182
3
4 Sequence preprocessing
185
4
5 Sequence assembly
189
3
6 Editing and finishing
192
5
7 Feature identification
197
3
8 Quality control
200
1
9 The finished sequence
200
1
10 Conclusion
201
1
11 Finding software on the Web
202
3
9 Human EST Sequences
205
10
Guy St C. Slater
1 Introduction
205
1
2 Background
205
1
3 Generation of the EST data
206
1
4 Reasons for EST sequencing
207
2
5 Publicly available EST data
209
2
6 EST analysis tools
211
1
7 Biological resources
212
1
8 WWW resources for ESTs
213
1
9 Summary
213
2
10 Prediction of Human Gene Structure
215
46
Luciano Milanesi
Igor B. Rogozin
1 Introduction
215
1
2 Genome structure
216
1
3 Approaches to evaluate prediction accuracy
217
2
4 Functional sites in nucleotide sequences
219
11
5 Functional regions in nucleotide sequences
230
6
6 Protein coding gene structure prediction
236
15
7 Analysis of potential proteins coded by predicted genes
251
1
8 RNA-coding gene structure prediction
252
1
9 Sequence analysis
252
9
11 Gene Finding: Putting the Parts Together
261
14
Anders Krogh
1 Introduction
261
1
2 Dynamic programming
262
4
3 State models
266
5
4 Performance comparison
271
1
5 Conclusion
272
3
12 Gene-Expression Databases
275
20
Duncan Davidson
Martin Ringwald
Christophe Dubreuil
1 Introduction
275
2
2 The scope of gene-expression databases
277
1
3 A survey of gene-expression data
278
6
4 A survey of gene-expression databases
284
8
5 The future of gene-expression databases
292
3
Index
295