Genetic Databases (eBook)

Front Cover 1
Genetics Databases 4
Copyright Page 5
Contents 6
Chapter 1. Introduction 16
1.1 Internet resources 16
1.2 Organisms and proteins 17
1.3 Phenotypes and genotypes 19
1.4 Physical mapping 21
1.5 Expression profiling 22
1.6 Multiprotein complexes and pathways 23
1.7 Sequence, structure and function 24
Chapter 2. Nucleic Acid and Protein Sequence Databases 26
2.1 Introduction 26
2.2 The main sequence databases 26
2.3 Rate of database growth 49
2.4 Problems with the data 50
2.5 Accessing the databases 52
References 52
Chapter 3. Phenotype, Mutation and Genetic Linkage Databases and Their Links to Sequence Databases 54
3.1 Introduction 54
3.2 Levels of variation 55
3.3 Definitions 55
3.4 Types of databases 56
3.5 Using mutation databases 64
3.6 Exercises 65
3.7 The HUGO mutation database initiative 66
3.8 Conclusion 66
References 67
Chapter 4. DNA Composition, Codon Usage and Exon Prediction 68
4.1 Introduction 68
4.2 Measures dependent on a model of coding DNA 70
4.3 Measures independent of a model of coding DNA 84
4.4 Coding statistics in gene identification programs 91
References 94
Chapter 5. The Properties of Amino Acids in Sequences 96
5.1 Introduction 96
5.2 Properties of amino acids 97
5.3 Empirically derived amino acid relationships 102
5.4 Relationship to the genetic code 107
5.5 Multiple sequence alignments 110
References 117
Chapter 6. Sequence Comparison 120
6.1 Introduction 120
6.2 Dotplots 122
6.3 Alignments 126
6.4 Motif-based approaches 130
6.5 Conclusion 133
References 134
Chapter 7. Simple Repetitive Sequences in DNA Databanks 136
7.1 Introduction 136
7.2 Microsatellites in databases for population genetic analyses 137
7.3 Genetic distances 142
7.4 Population sizes and gene flow 144
7.5 Tandem repeat block expansion diseases – a continuum from trinucleotides to minisatellites? Implications for database usage in population genetics 146
7.6 Summary 147
References 147
Chapter 8. Gene Feature Identification 150
8.1 Introduction 150
8.2 Biologically interesting sequences features 151
8.3 Sequence analysis methods 159
8.4 Computer programs, databases and WWW servers 167
8.5 An example 173
References 177
Chapter 9. Multiple Sequence Alignment 180
9.1 Introduction 180
9.2 Selecting the sequences to align 182
9.3 Automatic sequence alignment 184
9.4 Using Clustal W and Clustal X 187
9.5 Editing and viewing multiple alignments 196
References 197
Chapter 10. On-line Resources for RNA Science 200
10.1 Introduction 200
10.2 Specialized RNA-related databases 200
10.3 Tools for analysis: RNA structure and prediction 206
10.4 Future directions 207
References 209
Chapter 11. Predicting the Evolution, Structure and Function of Proteins from Sequence Information 214
11.1 Introduction 214
11.2 Protein evolution and function 214
11.3 Protein structure and function 217
11.4 Functions of enzymatic and regulatory domains 218
11.5 Classical genetics and protein functions 219
11.6 Summary 225
References 225
Chapter 12. Structural Databases 230
12.1 Introduction 230
12.2 The Brookhaven Protein Data Bank 231
12.3 The Cambridge Structural Database 231
12.4 BioMagResBank 232
12.5 The Nucleic Acid Database 232
12.6 A typical PDB entry 232
12.7 Protein structure classification resources 236
12.8 Methods for comparing protein structures 237
12.9 Available classification schemes 237
12.10 Constructing the CATH classification 238
12.11 Making use of structural databases 243
12.12 How does threading work? 248
12.13 Conclusions 252
References 253
Chapter 13. PKR – the Protein Kinase Resource 256
13.1 Introduction 256
13.2 Data definition 257
13.3 PKR functions and data 259
References 261
Chapter 14. Gene Expression Databases 262
14.1 Introduction 262
14.2 Gene-expression assays 264
14.3 Database scope 265
14.4 Gene-expression data 267
14.5 Access and submission 272
14.6 Specific database synopses 274
14.7 Conclusion 282
References 283
Chapter 15. Using the EcoCyc Database 284
15.1 Introduction 284
15.2 Genes 285
15.3 Proteins 288
15.4 Pathways 292
15.5 Summary 294
References 295
Appendix: List of URLs in Text and Tables 296
Index 304