Genetic Databases
Regular price
36.750 KD
inc. VAT
Couldn't load pickup availability
Table of contents
- Contentsv
- Chapter 1. Introduction1
- 1.1 Internet resources1
- 1.2 Organisms and proteins2
- 1.3 Phenotypes and genotypes4
- 1.4 Physical mapping6
- 1.5 Expression profiling7
- 1.6 Multiprotein complexes and pathways8
- 1.7 Sequence, structure and function9
- Chapter 2. Nucleic Acid and Protein Sequence Databases11
- 2.1 Introduction11
- 2.2 The main sequence databases11
- 2.3 Rate of database growth34
- 2.4 Problems with the data35
- 2.5 Accessing the databases37
- References37
- Chapter 3. Phenotype, Mutation and Genetic Linkage Databases and Their Links to Sequence Databases39
- 3.1 Introduction39
- 3.2 Levels of variation40
- 3.3 Definitions40
- 3.4 Types of databases41
- 3.5 Using mutation databases49
- 3.6 Exercises50
- 3.7 The HUGO mutation database initiative51
- 3.8 Conclusion51
- References52
- Chapter 4. DNA Composition, Codon Usage and Exon Prediction53
- 4.1 Introduction53
- 4.2 Measures dependent on a model of coding DNA55
- 4.3 Measures independent of a model of coding DNA69
- 4.4 Coding statistics in gene identification programs76
- References79
- Chapter 5. The Properties of Amino Acids in Sequences81
- 5.1 Introduction81
- 5.2 Properties of amino acids82
- 5.3 Empirically derived amino acid relationships87
- 5.4 Relationship to the genetic code92
- 5.5 Multiple sequence alignments95
- References102
- Chapter 6. Sequence Comparison105
- 6.1 Introduction105
- 6.2 Dotplots107
- 6.3 Alignments111
- 6.4 Motif-based approaches115
- 6.5 Conclusion118
- References119
- Chapter 7. Simple Repetitive Sequences in DNA Databanks121
- 7.1 Introduction121
- 7.2 Microsatellites in databases for population genetic analyses122
- 7.3 Genetic distances127
- 7.4 Population sizes and gene flow129
- 7.5 Tandem repeat block expansion diseases – a continuum from trinucleotides to minisatellites? Im131
- 7.6 Summary132
- References132
- Chapter 8. Gene Feature Identification135
- 8.1 Introduction135
- 8.2 Biologically interesting sequences features136
- 8.3 Sequence analysis methods144
- 8.4 Computer programs, databases and WWW servers152
- 8.5 An example158
- References162
- Chapter 9. Multiple Sequence Alignment165
- 9.1 Introduction165
- 9.2 Selecting the sequences to align167
- 9.3 Automatic sequence alignment169
- 9.4 Using Clustal W and Clustal X172
- 9.5 Editing and viewing multiple alignments181
- References182
- Chapter 10. On-line Resources for RNA Science185
- 10.1 Introduction185
- 10.2 Specialized RNA-related databases185
- 10.3 Tools for analysis: RNA structure and prediction191
- 10.4 Future directions192
- References194
- Chapter 11. Predicting the Evolution, Structure and Function of Proteins from Sequence Information199
- 11.1 Introduction199
- 11.2 Protein evolution and function199
- 11.3 Protein structure and function202
- 11.4 Functions of enzymatic and regulatory domains203
- 11.5 Classical genetics and protein functions204
- 11.6 Summary210
- References210
- Chapter 12. Structural Databases215
- 12.1 Introduction215
- 12.2 The Brookhaven Protein Data Bank216
- 12.3 The Cambridge Structural Database216
- 12.4 BioMagResBank217
- 12.5 The Nucleic Acid Database217
- 12.6 A typical PDB entry217
- 12.7 Protein structure classification resources221
- 12.8 Methods for comparing protein structures222
- 12.9 Available classification schemes222
- 12.10 Constructing the CATH classification223
- 12.11 Making use of structural databases228
- 12.12 How does threading work?233
- 12.13 Conclusions237
- References238
- Chapter 13. PKR – the Protein Kinase Resource241
- 13.1 Introduction241
- 13.2 Data definition242
- 13.3 PKR functions and data244
- References246
- Chapter 14. Gene Expression Databases247
- 14.1 Introduction247
- 14.2 Gene-expression assays249
- 14.3 Database scope250
- 14.4 Gene-expression data252
- 14.5 Access and submission257
- 14.6 Specific database synopses259
- 14.7 Conclusion267
- References268
- Chapter 15. Using the EcoCyc Database269
- 15.1 Introduction269
- 15.2 Genes270
- 15.3 Proteins273
- 15.4 Pathways277
- 15.5 Summary279
- References280
- Appendix: List of URLs in Text and Tables281
- Index289
Computer access is the only way to retrieve up-to-date sequences and this book shows researchers puzzled by the maze of URLs, sites, and searches how to use internet technology to find and analyze genetic data. The book describes the different types of databases, how to use a specific database to find a sequence that you need, and how to analyze the data to compare it with your own work.
The content also covers sequence phenotype, mutation, and genetic linkage databases; simple repetitive DNA sequences; gene feature identification; and prediction of structure and function of proteins from sequence information. This book will be invaluable to those starting a career in life sciences research as well as to established researchers wishing to make full use of available resources.
Key Features
* Describes a wide range of databases: DNA, RNA, protein, pathways, and gene expression
* Enables readers to access the information they need from databases on the web
* Includes a directory of URLs for easy reference
* Invaluable for those starting a career in life sciences research and also for established researchers wishing to make full use of available resources.
The content also covers sequence phenotype, mutation, and genetic linkage databases; simple repetitive DNA sequences; gene feature identification; and prediction of structure and function of proteins from sequence information. This book will be invaluable to those starting a career in life sciences research as well as to established researchers wishing to make full use of available resources.
Key Features
* Describes a wide range of databases: DNA, RNA, protein, pathways, and gene expression
* Enables readers to access the information they need from databases on the web
* Includes a directory of URLs for easy reference
* Invaluable for those starting a career in life sciences research and also for established researchers wishing to make full use of available resources.