Foundations of Comparative Genomics (eBook)

Arcady R. Mushegian (Autor)

eBook Download: PDF | EPUB

2010 | 1. Auflage
280 Seiten
Elsevier Science (Verlag)
978-0-08-054609-4 (ISBN)

Infos

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

Arcady R. Mushegian is Director of Bioinformatics at Stowers Institute for Medical Research in Kansas City and Professor of Microbiology at Kansas University Medical Center. He was born in Moscow, USSR, and graduated from Moscow State University.

Inhalt

Front Cover 1
Foundations of Comparative Genomics 4
Copyright Page 5
Contents 6
Dedication Page 8
Preface 10
Chapter 1: The Beginning of Computational Genomics 12
Chapter 2: Finding Sequence Similarities 16
Chapter 3: Homology: Can We Get It Right? 35
Glossary 42
Chapter 4: Getting Ready fot the Era of Comparative Genomics: The Importance of Viruses 44
Chapter 5: The First Fact of Comparative Genomics: Protein Sequences are Remarkably Resilient in Evolution 62
Chapter 6: The Second Fact of Comparative Genomics: Functional Convergence at the Molecular Level 81
Proteins with Same or Similar Functions 81
Proteins with Superficially Different Functions 82
Completely Uncharacterized Proteins 83
Analogous Function 84
Analogous Mechanism 84
Analogous Structure 85
Mechanisms of DOGs 90
DOGs and the Types of Homology 93
DOGs and Horizontal Gene Transfers 94
One-for-One and One-for-Many Relationships in DOGs 95
DOGs and Operons 95
DOGs and Gene Competition 96
DOGs, RNA–Protein Displacements, and RNA World 97
Detection of DOGs Using Phyletic Patterns and Phylogeny 98
Chapter 7: Prediction of Function and Reconstruction of Metabolism from Genomic Data: Homology-Based Approaches 102
Databases of Biochemical Information 104
Homology and Orthology: How to Use Them for Prediction of Protein Function, and What Can Go Wrong 105
Annotations by Homology and Errors Inherent in the Process 108
Placing Predicted Functions onto Metabolic Maps and Filling the Gaps 113
Chapter 8: Prediction of Function and Reconstruction of Metabolism: Post-Homology Approaches 116
Chapter 9: Structural Genomics:What Does It Tell Us about Life? 129
Chapter 10: How Many Protein Families are There? 150
Chapter 11: Phylogenetic Inference and the Era of Complete Genomes 162
Chapter 12: Two Stories about Evolution 189
Chapter 13: Minimal and Ancestral Genomes 211
Chapter 14: Comparative Genomics and Systems Biology 235
References 249
Index 270

Produkt-Details

• Erscheint lt. Verlag: 20.7.2010
• Sprache: englisch
• Themenwelt: Sachbuch/Ratgeber
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Medizin / Pharmazie ► Allgemeines / Lexika
• Themenwelt: Studium ► Querschnittsbereiche ► Epidemiologie / Med. Biometrie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Technik
• ISBN-10: 0-08-054609-9 / 0080546099
• ISBN-13: 978-0-08-054609-4 / 9780080546094