Bioinformatics : genes, proteins and computers / edited by Christine Orengo, David Jones, Janet Thornton.

Format:

Book

Contributor:

Orengo, Christine.

Jones, David (David T.)

Thornton, Janet M.

Series:

Advanced text

Language:

English

Subjects (All):

Bioinformatics.

Computational Biology--methods.

Genomics.

Proteomics.

Sequence Analysis--methods.

Medical Subjects:

Computational Biology--methods.

Genomics.

Proteomics.

Sequence Analysis--methods.

Physical Description:

xiv, 298 pages, 7 unnumbered pages of plates : illustrations (some color) ; 25 cm.

Place of Publication:

Oxford : BIOS Scientific ; New York : Distributed in the U.S. by Springer-Verlag, 2003.

Summary:

The Advanced Text series is designed for students taking advanced-level courses, including final year undergraduate and taught MSc. Books in this series will also be invaluable to researchers new to a field, and to established researchers as a basic reference text. Bioinformatics, the use of computers to address biological questions, has become an essential tool in biological research. It is one of the critical keys needed to unlock the information encoded in the flood of data generated by genome, protein structure, transcriptiome and proteome research. Bioinformatics covers both the more traditional approaches to the subject, including gene and protein sequence analysis and structure prediction, and more recent technologies such as datamining of transcriptomic and proteomic data, to provide insights on cellular mechanisms and the causes of disease.

Contents:

1. Molecular evolution / Sylvia Nagl 1

Molecular evolution is a fundamental part of bioinformatics 1

Evolution of protein families 9

Outlook: Evolution takes place at all levels of biological organization 15

2. Gene finding / John G. Sgouros, Richard M. Twyman 19

Finding genes in bacterial genomes 20

Finding genes in higher eukaryotes 21

Detecting non-coding RNA genes 27

3. Sequence comparison methods / Christine Orengo 29

Algorithms for pairwise sequence comparison 32

Fast database search methods 38

Assessing the statistical significance of sequence similarity 42

Intermediate sequence searching 44

Validation of sequence alignment methods by structural data 44

Multiple sequence alignment 45

4. Amino acid residue conservation / William S.J. Valdar, David T. Jones 49

Models of molecular evolution 49

Substitution matrices 50

Scoring residue conservation 57

Methods for scoring conservation 59

5. Function prediction from protein sequence / Sylvia B. Nagl 65

The similar sequence-similar structure-similar function paradigm 65

Functional annotation of biological sequences 66

Outlook: context-dependence of protein function 77

6. Protein structure comparison / Ian Sillitoe, Christine Orengo 81

Algorithms 84

Statistical methods for assessing structural similarity 99

Multiple structure comparison and 3-D templates for structural families 100

7. Protein structure classifications / Frances Pearl, Christine Orengo 103

Protocols used in classifying structures 104

Descriptions of the structural classification hierarchy 111

Overview of the populations in the different structural classifications and insights provided by the classifications 118

8. Comparative modeling / Andrew C.R. Martin 121

Why do comparative modeling? 121

Experimental methods 123

Evaluation of model quality 131

Factors influencing model quality 132

9. Protein structure prediction / David T. Jones 135

Strategies for protein structure prediction 135

Secondary structure prediction 138

Fold recognition methods 145

Ab initio prediction methods 149

Critically assessing protein structure prediction 149

10. From protein structure to function / Annabel E. Todd 151

Challenges of inferring function from structure 152

Methods of functional evolution 152

Functional classifications 154

From structure to function 156

Evolution of protein function from a structural perspective 164

Structural genomics 171

11. From structure-based genome annotation to understanding genes and proteins / Sarah A. Teichmann 175

Computational structural genomics: structural assignment of genome sequences 175

Methods and data resources for computational structural genomics 176

Proteome and protein evolution by computational structural genomics 181

Evolution of enzymes and metabolic pathways by structural annotation of genomes 186

12. Global approaches for studying protein-protein interactions / Sarah A. Teichmann 193

Protein-protein interactions 193

Experimental approaches for large-scale determination of protein-protein interactions 195

Structural analyses of domain interactions 196

The use of gene order to predict protein-protein interactions 198

The use of phylogeny to predict protein-protein interactions 200

13. Predicting the structure of protein-biomolecular interactions / Richard M. Jackson 203

Why predict molecular interactions? 203

Practical considerations 204

Molecular complementarity 204

The search problem 209

Conformational flexibility 211

Evaluation of models 214

Visualization methods 215

14. Experimental use of DNA arrays / Paul Kellam, Xiaohui Liu 217

Methods for large-scale analysis of gene expression 218

Using microarrays 219

Properties and processing of array data 221

Data normalization 223

Microarray standards and databases 226

15. Mining gene expression data / Xiaohui Liu, Paul Kellam 229

Data mining methods for gene expression analysis 230

Clustering 231

Classification 241

16. Proteomics / Malcolm P. Weir, Walter P. Blackstock, Richard M. Twyman 245

The proteome 245

Technology platforms in proteomics 246

17. Data managament of biological information / Nigel J. Martin 259

Data management concepts 260

Data management techniques 263

Challenges arising from biological data 270

18. Internet technologies for bioinformatics / Andrew C.R. Martin 273

Methods and standards 274.

Notes:

Includes bibliographical references and index.

ISBN:

1859960545

OCLC:

51805203