Guide to Human Genome Computing, 2nd edition

Front Cover......Page 1
Guide to Human Genome Computing......Page 4
Copyright Page......Page 5
Contents......Page 6
Contributors......Page 10
Preface......Page 14
1 Introduction......Page 16
2 Equipment for the tour......Page 17
3 Genome databases......Page 18
4 Analytic tools......Page 39
5 Conclusion......Page 53
6 URLs......Page 54
1 Introduction......Page 56
2 Genomic resources available......Page 57
4 CpG island libraries......Page 61
6 Probe and primer banks......Page 62
9 Backcross panels......Page 63
1 Introduction......Page 64
2 Fundamentals......Page 65
3 Modelling the domain......Page 70
4 Implementing the database......Page 74
5 Interfacing with analysis programs......Page 79
7 Further development......Page 88
2 Genetic identity-by-descent between sib-pairs......Page 90
3 Genetic identity-by-descent and recombination fraction......Page 92
4 Identity-by-descent distribution for an affected sib-pair......Page 93
5 Methods of affected sib-pair analysis......Page 96
6 Affected sib-pair analysis: strengths and limitations......Page 99
7 Conclusion......Page 100
List of computer programs......Page 102
1 Conservation of genes......Page 104
2 Conservation of linkage groups......Page 107
3 Value of comparative mapping......Page 109
4 Single-species databases......Page 110
5 Protein families......Page 122
6 Comparative mapping databases......Page 124
1 Introduction......Page 128
2 Background......Page 129
3 RH mapping concepts......Page 130
4 Radiation hybrid mapping programs......Page 134
5 Conclusions......Page 160
1 Introduction......Page 166
2 Strategy......Page 168
3 Software for sequence ready maps......Page 170
4 Long-range map construction (SAM, Z-RHMAPPER)......Page 171
5 STS-content data storage using ACEDB......Page 174
6 Sequence ready contig construction using FPC......Page 175
7 Process tracking and coordination......Page 187
8 Conclusions......Page 192
1 Introduction......Page 196
3 Gel image processing......Page 197
4 Sequence preprocessing......Page 200
5 Sequence assembly......Page 204
6 Editing and finishing......Page 207
7 Feature identification......Page 212
9 The finished sequence......Page 215
10 Conclusion......Page 216
11 Finding software on the Web......Page 217
2 Background......Page 220
3 Generation of the EST data......Page 221
4 Reasons for EST sequencing......Page 222
5 Publicly available EST data......Page 224
6 EST analysis tools......Page 226
7 Biological resources......Page 227
9 Summary......Page 228
1 Introduction......Page 230
2 Genome structure......Page 231
3 Approaches to evaluate prediction accuracy......Page 232
4 Functional sites in nucleotide sequences......Page 234
5 Functional regions in nucleotide sequences......Page 245
6 Protein coding gene structure prediction......Page 251
7 Analysis of potential proteins coded by predicted genes......Page 266
9 Sequence analysis......Page 267
1 Introduction......Page 276
2 Dynamic programming......Page 277
3 State models......Page 281
4 Performance comparison......Page 286
5 Conclusion......Page 287
1 Introduction......Page 290
2 The scope of gene-expression databases......Page 292
3 A survey of gene-expression data......Page 293
4 A survey of gene-expression databases......Page 299
5 The future of gene-expression databases......Page 307
Index......Page 310