Foundations of Comparative Genomics Book

Preface     ix
The Beginning of Computational Genomics     1
Finding Sequence Similarities     5
Homology: Can We Get It Right?     24
Getting Ready for the Era of Comparative Genomics: The Importance of Viruses     33
The First Fact of Comparative Genomics: Protein Sequences are Remarkably Resilient in Evolution     51
The Second Fact of Comparative Genomics: Functional Convergence at the Molecular Level     70
Prediction of Function and Reconstruction of Metabolism from Genomic Data: Homology-Based Approaches     91
Prediction of Function and Reconstruction of Metabolism: Post-Homology Approaches     105
Structural Genomics: What Does It Tell Us about Life?     118
How Many Protein Families are There?     139
Phylogenetic Inference and the Era of Complete Genomes     151
Two Stories about Evolution     178
Minimal and Ancestral Genomes     200
Comparative Genomics and Systems Biology     224
References     238
Index     259