| |
| |
| Preface | |
| |
| |
| Introduction: Personal Interludes | |
| |
| |
| |
| Genomes from Phage to Human | |
| |
| |
| |
| The humble beginnings | |
| |
| |
| |
| ...and the astonishing progress of genome sequencing | |
| |
| |
| |
| Basic questions of comparative genomics | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| The Evolutionary Concept in Genetics and Genomics | |
| |
| |
| |
| Similarity, homology, divergence and convergence | |
| |
| |
| |
| The critical definitions | |
| |
| |
| |
| Conservation of protein sequence and structure in evolution | |
| |
| |
| |
| Homologs: orthologs and paralogs | |
| |
| |
| |
| Patterns and mechanisms in genome evolution | |
| |
| |
| |
| Evolution of gene order | |
| |
| |
| |
| Lineage-specific gene loss | |
| |
| |
| |
| Lineage-specific expansion of gene families | |
| |
| |
| |
| Horizontal (lateral) gene transfer | |
| |
| |
| |
| Non-orthologous gene displacement and the minimal gene set concept | |
| |
| |
| |
| Phyletic patterns (profiles) | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Information Sources for Genomics | |
| |
| |
| |
| General purpose sequence databases | |
| |
| |
| |
| Nucleotide sequence databases | |
| |
| |
| |
| Protein sequence databases | |
| |
| |
| |
| Reliability of the database entries | |
| |
| |
| |
| Protein sequence motifs and domain databases | |
| |
| |
| |
| Motif databases | |
| |
| |
| |
| Domain databases | |
| |
| |
| |
| Integrated motif and domain databases | |
| |
| |
| |
| Protein structure databases | |
| |
| |
| |
| Specialized genomics databases | |
| |
| |
| |
| Organism-specific databases | |
| |
| |
| |
| Prokaryotes | |
| |
| |
| |
| Unicellular eukaryotes | |
| |
| |
| |
| Multicellular eukaryotes | |
| |
| |
| |
| Taxonomy, protein interactions, and other databases | |
| |
| |
| |
| Taxonomy databases | |
| |
| |
| |
| Signal transduction and protein interaction databases | |
| |
| |
| |
| Biochemical databases | |
| |
| |
| |
| PubMed | |
| |
| |
| |
| Specifying the terms in PubMed search | |
| |
| |
| |
| Interpretation of the search pattern | |
| |
| |
| |
| NCBI Bookshelf | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Principles and Methods of Sequence Analysis | |
| |
| |
| |
| Identification of genes in a genomic DNA sequence | |
| |
| |
| |
| Prediction of protein-coding genes | |
| |
| |
| |
| Algorithms and software tools for gene identification | |
| |
| |
| |
| Principles of sequence similarity searches | |
| |
| |
| |
| Substitution scores and substitution matrices | |
| |
| |
| |
| Statistics of protein sequence comparison | |
| |
| |
| |
| Protein sequence complexity. Compositional bias | |
| |
| |
| |
| Algorithms for sequence alignment and similarity search | |
| |
| |
| |
| The basic alignment concepts and principal algorithms | |
| |
| |
| |
| Sequence database search algorithms | |
| |
| |
| |
| Motifs, domains and profiles | |
| |
| |
| |
| Practical issues: how to get the most out of BLAST | |
| |
| |
| |
| Setting up the BLAST search | |
| |
| |
| |
| Choosing the BLAST parameters | |
| |
| |
| |
| Running BLAST and formatting the output | |
| |
| |
| |
| Analysis and interpretation of BLAST results | |
| |
| |
| |
| The road to discovery | |
| |
| |
| |
| Protein annotation in the absence of detectable homologs | |
| |
| |
| |
| Prediction of subcellular localization of the protein | |
| |
| |
| |
| Prediction of structural features of the protein | |
| |
| |
| |
| Threading | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Genome Annotation and Analysis | |
| |
| |
| |
| Methods, approaches and results in genome annotation | |
| |
| |
| |
| Genome annotation: data flow and performance | |
| |
| |
| |
| Automation of genome annotation | |
| |
| |
| |
| Accuracy of genome annotation | |
| |
| |
| |
| A case study on genome annotation | |
| |
| |
| |
| Genome context analysis and functional prediction | |
| |
| |
| |
| Phyletic patterns (profiles) | |
| |
| |
| |
| Gene (domain) fusions: "Rosetta Stone" | |
| |
| |
| |
| Gene clusters and genomic neighborhoods | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Comparative Genomics and New Evolutionary Biology | |
| |
| |
| |
| The three domains of life | |
| |
| |
| |
| Prevalence of lineage-specific gene loss and horizontal gene transfer | |
| |
| |
| |
| The Tree of Life: before and after the genomes | |
| |
| |
| |
| Phylogenetic trees in the pre-genomic era | |
| |
| |
| |
| Comparative genomics threatens the species tree concept | |
| |
| |
| |
| Genome trees - can comparative genomics help build a consensus? | |
| |
| |
| |
| The genomic clock | |
| |
| |
| |
| The major transitions in evolution: a comparative-genomic perspective | |
| |
| |
| |
| Ancestral life form and evolutionary reconstructions | |
| |
| |
| |
| Beyond LUCA, back to the RNA world | |
| |
| |
| |
| A brief history of early life | |
| |
| |
| |
| The prokaryote-eukaryote transition and origin of novelty in eukaryotes | |
| |
| |
| |
| Conclusions and outlook: evolution tinkers with fluid genomes | |
| |
| |
| |
| Further Reading | |
| |
| |
| |
| Evolution of Central Metabolic Pathways: The Playground of Non-orthologous Gene Displacement | |
| |
| |
| |
| Carbohydrate metabolism | |
| |
| |
| |
| Glycolysis | |
| |
| |
| |
| Gluconeogenesis | |
| |
| |
| |
| Entner-Doudoroff pathway and pentose phosphate shunt | |
| |
| |
| |
| TCA cycle | |
| |
| |
| |
| Pyrimidine biosynthesis | |
| |
| |
| |
| Purine biosynthesis | |
| |
| |
| |
| Amino acid biosynthesis | |
| |
| |
| |
| Biosynthesis of aromatic amino acids | |
| |
| |
| |
| Arginine biosynthesis | |
| |
| |
| |
| Histidine biosynthesis | |
| |
| |
| |
| Biosynthesis of branched-chain amino acids | |
| |
| |
| |
| Proline biosynthesis | |
| |
| |
| |
| Coenzyme biosynthesis | |
| |
| |
| |
| Thiamin | |
| |
| |
| |
| Riboflavin | |
| |
| |
| |
| NAD | |
| |
| |
| |
| Biotin | |
| |
| |
| |
| Heme | |
| |
| |
| |
| Pyridoxine | |
| |
| |
| |
| Microbial enzymes as drug targets | |
| |
| |
| |
| Potential targets for broad-spectrum drugs | |
| |
| |
| |
| Potential targets for pathogen-specific drugs | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Genomes and the Protein Universe | |
| |
| |
| |
| The protein universe is highly structured and there are few common folds | |
| |
| |
| |
| Counting the beans: structural genomics, distributions of protein folds and superfamilies in genomes and some models of genome evolution | |
| |
| |
| |
| Evolutionary dynamics of multidomain proteins | |
| |
| |
| |
| Conclusions and outlook | |
| |
| |
| |
| Further reading | |
| |
| |
| |
| Epilogue: Peering through the crystal ball | |
| |
| |
| |
| Functional genomics: a programme of prediction-driven research? | |
| |
| |
| |
| Digging up genomic junkyards | |
| |
| |
| |
| "Dreams of a final theory" | |
| |
| |
| Appendices | |
| |
| |
| |
| Glossary | |
| |
| |
| |
| Useful WWW sites | |
| |
| |
| Databases | |
| |
| |
| Major genome sequencing centers | |
| |
| |
| |
| Problems | |
| |
| |
| References | |
| |
| |
| Index | |