Copyright © 2003, Kluwer Academic.
NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.
Bookshelf ID: NBK20260PMID: 21089240
Sequence - Evolution - Function
Computational Approaches in Comparative Genomics
Eugene V Koonin and Michael Y Galperin.
National Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health
Boston: Kluwer Academic; 2003.
ISBN-10: 1-40207-274-0
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.
Contents
- Preface
- Introduction: Personal Interludes
- Chapter 1. Genomics: From Phage to Human
- Chapter 2. Evolutionary Concept in Genetics and Genomics
- Chapter 3. Information Sources for Genomics
- Chapter 4. Principles and Methods of Sequence Analysis
- 4.1 Identification of Genes in a Genomic DNA Sequence
- 4.2 Principles of Sequence Similarity Searches
- 4.3 Algorithms for Sequence Alignment and Similarity Search
- 4.4 Practical Issues: How to Get the Most Out of BLAST
- 4.5 The Road to Discovery
- 4.6 Protein Annotation in the Absence of Detectable Homologs
- 4.7 Conclusions and Outlook
- 4.8 Further Reading
- Chapter 5. Genome Annotation and Analysis
- Chapter 6. Comparative Genomics and New Evolutionary Biology
- 6.1 The Three Domains of Life
- 6.2 Prevalence of Lineage-specific Gene Loss and Horizontal Gene Transfer in Evolution
- 6.3 The Tree of Life: Before and After the Genomes
- 6.4 The Major Transitions in Evolution: A Comparative-Genomic Perspective
- 6.5 Conclusions and Outlook: Evolution Tinkers with Fluid Genomes
- 6.6 Further Reading
- Chapter 7. Evolution of Central Metabolic Pathways: The Playground of Non-Orthologous Gene Displacement
- Chapter 8. Genomes and the Protein Universe
- 8.1 The Protein Universe Is Highly Structured and There Are Few Common Folds
- 8.2 Counting the Beans: Structural Genomics, Distributions of Protein Folds and Superfamilies in Genomes and Some Models of Genome Evolution
- 8.3 Evolutionary Dynamics of Multidomain Proteins and Domain Accretion
- 8.4 Conclusions and Outlook
- 8.5 Further reading
- Chapter 9. Epilogue: Peering through the Crystal Ball
- Appendixes
- References
- Review Taking a functional genomics approach in molecular medicine.[Trends Mol Med. 2001]Yaspo ML. Trends Mol Med. 2001 Nov; 7(11):494-501.
- Review [Computational approaches to microRNA discovery].[Yi Chuan. 2008]Hou YYYing XM, Li WJ, . Yi Chuan. 2008 Jun; 30(6):687-96.
- Review Proteomics in the chicken: tools for understanding immune responses to avian diseases.[Poult Sci. 2004]Review Proteomics in the chicken: tools for understanding immune responses to avian diseases.Burgess SC. Poult Sci. 2004 Apr; 83(4):552-73.
- Review Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics.[Res Microbiol. 2000]Review Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics.Benner SAChamberlin SG, Liberles DA, Govindarajan S, Knecht L, . Res Microbiol. 2000 Mar; 151(2):97-106.
- Review A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.[Mol Biol Evol. 2000]Review A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.Pollock DDEisen JA, Doggett NA, Cummings MP, . Mol Biol Evol. 2000 Dec; 17(12):1776-88.
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