Ancestral Sequence Reconstruction

Hardcover | May 31, 2007

EditorDavid A Liberles

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Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potentialapplications in a range of fields. Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methodsfor reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationallyreconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research. This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in thefields of molecular biology, molecular evolution, and evolutionary bioinformatics.

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Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potentialapplications in a range of fields. Ancest...

David A. Liberles is Assistant Professor at the Department of Molecular Biology, University of Wyoming, USA

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Format:HardcoverDimensions:272 pages, 9.69 × 7.44 × 0.71 inPublished:May 31, 2007Publisher:Oxford University PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:0199299188

ISBN - 13:9780199299188

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Table of Contents

1. Steven A. Benner: The Early Days of Paleogenomics, Connecting Molecules to the Planet2. Eric A. Gaucher: Ancestral Sequence Reconstruction as a Tool to Understand Natural History and Guide Synthetic Biology: Realizing and Extending the Vision of Zuckerkandl and Pauling3. Janos T. Kodra, Marie Skovgaard, Dennis Madsen, and David A. Liberles: Linking Sequence to Function in Drug Design with Ancestral Sequence Reconstruction4. Tal Pupko, Adi Doron-Faigenboim, David A. Liberles, and Gina M. Cannarozzi: Probabilistic Models and Their Impact on the Accuracy of Reconstructed Ancestral Sequences5. Gina M. Cannarozzi, Adrian Schneider, and Gaston H. Gonnet: Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution- Algorithms and Applications6. Jonathan P. Bollback, Paul P. Gardner, and Rasmus Nielsen: Estimating the History of Mutations on a Phylogeny7. F. Nicholas Braun: Coarse Projections of the Protein-Mutational Fitness Landscape8. David D. Pollock and Belinda S. W. Chang: Dealing with Uncertainty in Ancestral Sequence Reconstruction: Sampling from the Posterior Distribution9. Lesley J. Collins and Peter J. Lockhart: Evolutionary Properties of Sequences and Ancestral State Reconstruction10. Mary J. O'Connell and James O. McInerney: Reconstructing the Ancestral Eukaryote- Lessons from the Past11. Xun Gu, Ying Zheng, Yong Huang, and Dongping Xu: Using Ancestral Sequence Inference to Determine the Trend of Functional Divergence After Gene Duplication12. Toni Gabaldon and Martijn A. Huynen: Reconstruction of Ancestral Proteomes13. Etienne G. J. Danchin, Eric A. Gaucher, and Pierre Pontarotti: Computational Reconstruction of Ancestral Genomic Regions from Evolutionarily Conserved Gene Clusters14. Eric A. Gaucher: Experimental Resurrection of Ancient Biomolecules: Gene Synthesis, Heterologous Protein Expression, and Functional Assays15. Belinda S. W. Chang, Mikhail V. Matz, Steven F. Field, Johannes Muller, and Ilke van Hazel: Dealing with Model Uncertainty in Reconstructing Ancestral Proteins in the Laboratory: Examples from Ancestral Visual Pigments and GFP-like Proteins16. Joseph W. Thornton and Jamie T. Bridgham: Unraveling the Evolution of Complexity by Resurrecting Ancient Genes17. Dawn J. Brooks and Eric A. Gaucher: A Thermophilic Last Universal Ancestor Inferred from its Estimated Amino Acid Composition18. Slim O. Sassi and Steven A. Benner: The Resurrection of Ribonucleases from Mammals. From Ecology to Medicine19. Denis C. Shields, Kate Johnston, Iain M. Wallace, and Richard J. Edwards: Evolution of Specificity and Diversity