Handbook of comparative genomics : principles and methodology / Cecilia Saccone, Graziano Pesole.

Format:

Book

Author/Creator:

Saccone, C.

Contributor:

Pesole, Graziano.

Language:

English

Subjects (All):

Genomics--Handbooks, manuals, etc.

Genomics.

Evolutionary genetics--Handbooks, manuals, etc.

Evolutionary genetics.

Computational Biology.

Evolution, Molecular.

Sequence Analysis, DNA.

Medical Subjects:

Genomics.

Computational Biology.

Evolution, Molecular.

Sequence Analysis, DNA.

Genre:

Handbooks and manuals.

Physical Description:

xiv, 427 pages : illustrations ; 26 cm

Other Title:

Comparative genomics

Place of Publication:

New York : Wiley-Liss, [2003]

Summary:

Handbook of Comparative Genomics: Principles and Methodology is a practical text for students and researchers covering basic and applied problems in the emerging field of comparative functional genomics. It offers a comparative perspective on the state of the art and key principles of genome sequencing, expression, evolution, and phylogenetics in organelles, prokaryotes, model organisms, and humans. Moreover, the Handbook provides a unique and thorough treatment of biological databases, analysis of the transcriptome and proteome, and the bioinformatic approaches for comparative genome analysis.

The text begins with an introduction to important features of completely sequenced genomes from mitochondria, C. elegans and Arabidopsis to Drosophila and humans. The next section covers cutting-edge analytic approaches involving ESTs, SAGE, DNA microarrays, protein biochips, and 2D gel electrophoresis. The following section deals comprehensively with computational approaches to comparative genome and proteome sequence analysis, including sequence assembly, pattern searching, gene and protein function prediction, and structure prediction. The text concludes with a section discussing genome evolution and molecular phylogenetics. This timely and cutting-edge text also: Presents both the concepts and methodology of comparative genomics Reviews the basic principles of genomics and gene expression analysis Covers the bioinformatics approaches to comparative analysis Discusses analytic methods in proteomics and transcriptomics Includes a comprehensive list of Web resources

The authors draw upon their wealth of teaching and research experience to offer a coherent presentation appropriate forstudents, trainees, researchers, and scientists across the life sciences.

Contents:

I Genome Features 1

1 Prokaryotes 3

1.2 Morphology and Classification 8

1.3 Genome Shape and Size 10

1.4 Gene Content and Organization 16

1.5 Base Composition 20

1.6 Codon Use 27

1.7 Replication and Expression 29

2 Eukaryotes 36

2.2 Classification and Time Scale 36

2.3 Genome Shape and Size 40

2.4 Base Composition 46

2.5 Replication, Repair, and Recombination 48

2.6 Gene Expression 53

2.6.1 Transcription and Posttranscriptional Regulation 53

2.6.2 Genetic Code and Codon Use 59

2.6.3 Translation and Posttranslation Modifications 61

2.7 Completely Sequenced Eukaryotic Genomes 64

2.7.1 Saccharomyces cerevisiae Genome 66

2.7.2 Schizosaccharomyces pombe Genome 69

2.7.3 Caenorhabditis elegans Genome 70

2.7.4 Drosophila melanogaster Genome 72

2.7.5 Arabidopsis thaliana Genome 74

2.7.6 Oryza sativa Genome 77

2.7.7 Homo sapiens Genome 78

3 Organelles 85

3.1 Mitochondria 85

3.1.1 General Structure and Function 85

3.1.2 DNA and Genetic System 88

3.1.3 Genome Features 97

3.2 Chloroplasts and Other Plastids 125

II Methodologies 131

4 Molecular Biology Techniques for Genomics 133

4.1 Genome DNA Sequencing 133

4.1.1 DNA-Sequencing Techniques 133

4.1.2 The Human Genome Project 136

4.2 Analysis of the Transcriptome 137

4.2.1 Analysis of Gene Expression 137

4.2.2 Expressed Sequence Tags 138

4.2.3 Serial Analysis of Gene Expression 139

4.2.4 Differential Display 141

4.2.5 Representional Difference Analysis 142

4.2.6 DNA Microarrays 143

4.3 Analysis of the Proteome 149

4.3.1 Two-Dimensional Gel Electrophoresis 151

4.3.2 Protein Identification 151

4.3.3 Study of Protein-DNA and Protein-Protein Interactions 155

4.3.4 Proteome Analysis Using Biochips 157

5 Biological Databases in the Genomic Era 159

5.2 Primary and Specialized Databases 159

5.3 Database Structures 162

5.4 Linked Databases and Database Interoperability 163

5.5 Database Annotation 166

5.6 Retrieval Systems 169

5.6.1 SRS 169

5.6.2 Entrez 169

5.6.3 Other Retrieval Systems 170

5.7 Nucleotide Databases 170

5.8 Protein Databases 171

5.9 Other Protein Databases 171

5.10 Genomic Databases and Resources 174

5.11 Gene Databases and Resources 179

5.12 Transcriptome Databases 180

5.13 Metabolism Databases 181

5.14 Mutation Databases 182

5.15 Mitochondrial Databases and Resources 184

6 Computational Methods for the Analysis of Genome Sequence Data 187

6.2 Dot-Plot Matrix 188

6.3 Sequence Pairwise Alignment 189

6.3.1 Needleman-Wunsch Global Alignment Algorithm 191

6.3.2 Smith-Waterman Algorithm for the Identification of Common Molecular Subsequences 193

6.3.3 Alignment of cDNA and Genomic DNA Sequences 196

6.3.4 Genome Alignment 198

6.3.5 Cleanup of Sequence Databases from Redundancy 201

6.3.6 Measure of the Similarity Degree between Homologous Sequences 203

6.4 Database Searching 208

6.4.1 FASTA 209

6.4.2 BLAST 211

6.4.3 BLAST and FASTA Family of Programs 215

6.4.4 Filtering Matches to Unwanted Sequences 216

6.4.5 Filtering Matches to Repetitive Sequences 221

6.4.6 Statistical Significance of Alignment Scores 223

6.5 Multiple Alignment 226

6.6 Alignment Profiles to Recognize Distantly Related Protein or Protein Modules 230

6.7 Methods for Sequence Assembly 234

6.7.1 Sequence Cleaning 236

6.7.2 Sequence Clustering 237

6.7.3 Construction of Alignment Consensus 238

6.7.4 Sequence Mapping by Electronic PCR 240

6.7.5 Sequence Assembly in Genome and EST Projects 240

6.7.6 Sequence Assembly for Gene Index Construction 243

6.8 Linguistic Analysis of Biosequences 245

6.8.1 Biosequences as Markov Chains 248

6.8.2 Linguistic Complexity of Biosequences 249

6.8.3 Identification of Repeats in Genomic Sequences 253

6.8.4 Pattern Searching in Biosequences 254

6.8.5 Identification of Promoter Regions in Chromosomal Sequences 261

6.8.6 Pattern Discovery for the Identification of Gene Regulatory Elements and of Protein Motif Models 262

6.8.7 Gene Prediction 265

6.8.8 Identification of CpG Islands in Genomic Sequences 269

6.8.9 Analysis of Codon Use Strategy 271

6.9 Prediction of RNA Secondary Structures 273

6.10 Protein Sequence Analysis 280

6.10.1 Analysis of Protein Primary Sequences 281

6.10.2 Prediction of Transmembrane Protein Helices 285

6.10.3 Identification of Protein Signal Peptides and Prediction of Their Subcellular Location 290

6.10.4 Prediction of Protein Secondary Structure 293

6.10.5 Prediction of Coiled-Coil and Helix-Turn-Helix Structures 298

6.10.6 Prediction of Protein Tertiary Structure 300

6.10.7 Protein Fold Recognition and Classification 302

6.10.8 Comparative Evolutionary Genomic Tools for Predicting Protein Function 303

6.11 Evolutionary and Phylogenetic Analysis 306

6.11.1 Estimating Genetic Distances between Homologous Sequences 306

6.11.2 Molecular Phylogeny 309

III Comparative Genomics 325

7 Molecular Evolution 327

7.2 Evolution of Genome Size 328

7.3 Role of Base Composition in Evolution 332

7.4 Evolution of the Prokaryotic Genome 337

7.5 From Prokaryotes to Eukaryotes 338

7.5.1 Origin of the Eukaryotic Cell 338

7.5.2 Evolution of the Mitochondrial Genome 340

7.5.3 Origin and Evolution of Plastids 346

7.6 From Unicellular to Multicellular State 349

7.7 Evolution of the Nuclear Genome 351

7.7.1 Introns 351

7.7.2 Gene and Protein Number 352

7.7.3 Noncoding Elements 353

7.7.4 Expansion of Gene Families 353

7.7.5 Genome Duplication 360

8 Molecular Phylogeny 362

8.2 Molecular Clock 363

8.3 Similarity Measure: Orthology Versus Paralogy 364

8.4 Molecular Phylogeny in the Genomics Era 367

8.5 Interrelationships between Distant Taxa: The Tree of Life 369

8.6 Phylogeny of Metazoans 370

8.6.1 Organellar versus Nuclear Taxonomy 370

8.6.2 Phylogeny of Mammals 371

Appendix URLs Cited in the Text 375.

Notes:

Includes bibliographical references (pages 377-422) and index.

ISBN:

047139128X

OCLC:

50843482