Elsevier S & T

Foundations of Comparative Genomics

Mushegian, Arcady R.

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Table of contents
  • Foundations of Comparative Genomicsiii
  • Copyright Pageiv
  • Contentsv
  • Dedication Pagevii
  • Prefaceix
  • Chapter 1: The Beginning of Computational Genomics1
  • Chapter 2: Finding Sequence Similarities5
  • Chapter 3: Homology: Can We Get It Right?24
  • Glossary31
  • Chapter 4: Getting Ready fot the Era of Comparative Genomics: The Importance of Viruses33
  • Chapter 5: The First Fact of Comparative Genomics: Protein Sequences are Remarkably Resilient in Evo51
  • Chapter 6: The Second Fact of Comparative Genomics: Functional Convergence at the Molecular Level70
  • Proteins with Same or Similar Functions70
  • Proteins with Superficially Different Functions71
  • Completely Uncharacterized Proteins72
  • Analogous Function73
  • Analogous Mechanism73
  • Analogous Structure74
  • Mechanisms of DOGs79
  • DOGs and the Types of Homology82
  • DOGs and Horizontal Gene Transfers83
  • One-for-One and One-for-Many Relationships in DOGs84
  • DOGs and Operons84
  • DOGs and Gene Competition85
  • DOGs, RNA–Protein Displacements, and RNA World86
  • Detection of DOGs Using Phyletic Patterns and Phylogeny87
  • Chapter 7: Prediction of Function and Reconstruction of Metabolism from Genomic Data: Homology-Based91
  • Databases of Biochemical Information93
  • Homology and Orthology: How to Use Them for Prediction of Protein Function, and What Can Go Wrong94
  • Annotations by Homology and Errors Inherent in the Process97
  • Placing Predicted Functions onto Metabolic Maps and Filling the Gaps102
  • Chapter 8: Prediction of Function and Reconstruction of Metabolism: Post-Homology Approaches105
  • Chapter 9: Structural Genomics:What Does It Tell Us about Life?118
  • Chapter 10: How Many Protein Families are There?139
  • Chapter 11: Phylogenetic Inference and the Era of Complete Genomes151
  • Chapter 12: Two Stories about Evolution178
  • Chapter 13: Minimal and Ancestral Genomes200
  • Chapter 14: Comparative Genomics and Systems Biology224
  • References238
  • Index259
Book details
  • Vendor Elsevier S & T
  • SKU 9780120887941
  • ISBN-13 9780080546094
  • Author Mushegian, Arcady R.
  • Category Medical
  • Subject Biostatistics

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This book provides an overview of computational analysis of genes and genomes, and of some most notable findings that come out of this work. Foundations of Comparative Genomics presents a historical perspective, beginning with early analysis of individual gene sequences, to present day comparison of gene repertoires encoded by completely sequenced genomes. The author discusses the underlying scientific principles of comparative genomics, argues that completion of many genome sequences started a new era in biology, and provides a personal view on several state-of-the-art issues, such as systems biology and whole-genome phylogenetic reconstructions. This book is an essential reference for researchers and students in computational biology, evolutionary biology, and genetics.

* Presents an historic overview of genome biology and its achievements

* Includes topics not covered in other books such as minimal and ancestral genomes

* Discusses the evolutionary resilience of protein-coding genes and frequent functional convergence at the molecular level

* Critically reviews horizontal gene transfer and other contentious issues

* Covers comparative virology as a somewhat overlooked foundation of modern genome science