Ancestral Sequence Reconstruction

Author : David A Liberles
Publisher : Oxford University Press on Demand
Page : 267 pages
File Size : 48,8 Mb
Release : 2007-05-31
Category : Science
ISBN : 9780199299188

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Ancestral Sequence Reconstruction by David A Liberles Pdf

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 potential applications 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 methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including wholeproteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed 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 toprovide 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 the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.

Author : David A Liberles
Publisher : OUP Oxford
Page : 266 pages
File Size : 54,8 Mb
Release : 2007-05-31
Category : Science
ISBN : 9780191538414

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Ancestral Sequence Reconstruction by David A Liberles Pdf

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 potential applications 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 methods for 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 computationally reconstructed 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 the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.

Author : Susumu Ohno
Publisher : Springer Science & Business Media
Page : 171 pages
File Size : 54,7 Mb
Release : 2013-12-11
Category : Medical
ISBN : 9783642866593

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Evolution by Gene Duplication by Susumu Ohno Pdf

It is said that "necessity is the mother of invention". To be sure, wheels and pulleys were invented out of necessity by the tenacious minds of upright citi zens. Looking at the history of mankind, however, one has to add that "Ieisure is the mother of cultural improvement". Man's creative genius flourished only when his mind, freed from the worry of daily toils, was permitted to entertain apparently useless thoughts. In the same manner, one might say with regard to evolution that "natural selection mere(y tnodifted, while redundanry created". Natural selection has been extremely effective in policing alleHe mutations which arise in already existing gene loci. Because of natural selection, organisms have been able to adapt to changing environments, and by adaptive radiation many new species were created from a common ancestral form. Y et, being an effective policeman, natural selection is extremely conservative by nature. Had evolution been entirely dependent upon natural selection, from a bacterium only numerous forms of bacteria would have emerged. The creation of metazoans, vertebrates and finally mammals from unicellular organisms would have been quite impos sible, for such big leaps in evolution required the creation of new gene loci with previously nonexistent functions. Only the cistron which became redun dant was able to escape from the relentless pressure of natural selection, and by escaping, it accumulated formerly forbidden mutations to emerge as a new gene locus.

Author : Tobias Sikosek
Publisher : Humana
Page : 0 pages
File Size : 53,6 Mb
Release : 2018-10-09
Category : Science
ISBN : 1493987356

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Computational Methods in Protein Evolution by Tobias Sikosek Pdf

This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.

Author : Gina M. Cannarozzi,Adrian Schneider
Publisher : Oxford University Press
Page : 297 pages
File Size : 40,8 Mb
Release : 2012-02-23
Category : Mathematics
ISBN : 9780199601165

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Codon Evolution by Gina M. Cannarozzi,Adrian Schneider Pdf

The second part of the book focuses on codon usage bias.

Author : Jay F. Storz
Publisher : Oxford University Press
Page : 272 pages
File Size : 44,5 Mb
Release : 2018-11-08
Category : Science
ISBN : 9780192538765

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Hemoglobin by Jay F. Storz Pdf

The primary aim of this book is to provide a synthesis of our current understanding of hemoglobin function and evolution, and to illustrate how research on one particular family of proteins has provided general insights into mechanisms of protein evolution and biochemical adaptation. In doing so, it will also promote an appreciation of how mechanistic insights into protein function can enrich our understanding of how evolution works. Reciprocally, it highlights how approaches in evolutionary genetics (such as phylogenetic comparative methods and ancestral sequence reconstruction) can be brought to bear on questions about the functional evolution of proteins. This treatise on the functional evolution of hemoglobin illustrates how research on a single, well-chosen model system can enhance our investigative acuity and bring key conceptual questions into especially sharp focus.

Author : Eugene V. Koonin,Michael Galperin
Publisher : Springer Science & Business Media
Page : 482 pages
File Size : 51,5 Mb
Release : 2013-06-29
Category : Science
ISBN : 9781475737837

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Sequence — Evolution — Function by Eugene V. Koonin,Michael Galperin Pdf

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. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 41,5 Mb
Release : 2009-03-26
Category : Science
ISBN : 9780521877107

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The Phylogenetic Handbook by Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey Pdf

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Author : A. Thomas
Publisher : Unknown
Page : 128 pages
File Size : 54,6 Mb
Release : 2019
Category : Electronic
ISBN : OCLC:1108705132

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Ancestral Sequence Reconstruction as an Accessible Tool for the Engineering of Biocatalyst Stability by A. Thomas Pdf

Author : Roderick D.M. Page,Edward C. Holmes
Publisher : John Wiley & Sons
Page : 352 pages
File Size : 44,9 Mb
Release : 2009-07-14
Category : Science
ISBN : 9781444313369

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Molecular Evolution by Roderick D.M. Page,Edward C. Holmes Pdf

The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.

Author : Miguel Alcalde
Publisher : Springer
Page : 286 pages
File Size : 51,5 Mb
Release : 2017-02-14
Category : Science
ISBN : 9783319504131

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Directed Enzyme Evolution: Advances and Applications by Miguel Alcalde Pdf

This book focuses on some of the most significant advances in enzyme engineering that have been achieved through directed evolution and hybrid approaches. On the 25th anniversary of the discovery of directed evolution, this volume is a tribute to the pioneers of this thrilling research field, and at the same time provides a comprehensive overview of current research and the state of the art. Directed molecular evolution has become the most reliable and robust method to tailor enzymes, metabolic pathways or even whole microorganisms with improved traits. By mirroring the Darwinian algorithm of natural selection on a laboratory scale, new biomolecules of invaluable biotechnological interest can now be engineered in a manner that surpasses the boundaries of nature. The volume is divided into two sections, the first of which provides an update on recent successful cases of enzyme ensembles from different areas of the biotechnological spectrum, including tryptophan synthases, unspecific peroxygenases, phytases, therapeutic enzymes, stereoselective enzymes and CO2-fixing enzymes. This section also provides information on the directed evolution of whole cells. The second section of the book summarizes a variety of the most applicable methods for library creation, together with the future trends aimed at bringing together directed evolution and in silico/computational enzyme design and ancestral resurrection.

Author : Guangchuang Yu
Publisher : Unknown
Page : 128 pages
File Size : 49,6 Mb
Release : 2022
Category : Phylogeny
ISBN : 1032245549

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Data Integration, Manipulation and Visualization of Phylogenetic Trees by Guangchuang Yu Pdf

"Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra. Using the most comprehensive packages for phylogenetic data integration and visualization, contains numerous examples that can be used for teaching and learning. Ideal for undergraduate readers and researchers with a working knowledge of R and ggplot2"--

Author : Masatoshi Nei,Sudhir Kumar
Publisher : Oxford University Press
Page : 352 pages
File Size : 50,7 Mb
Release : 2000-07-27
Category : Science
ISBN : 9780199881222

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Molecular Evolution and Phylogenetics by Masatoshi Nei,Sudhir Kumar Pdf

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Author : Ziheng Yang
Publisher : Oxford University Press
Page : 509 pages
File Size : 54,7 Mb
Release : 2014
Category : Science
ISBN : 9780199602605

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Molecular Evolution by Ziheng Yang Pdf

This book presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. The book offers numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative.

Author : Mourad Elloumi,Costas Iliopoulos,Jason T. L. Wang,Albert Y. Zomaya
Publisher : John Wiley & Sons
Page : 656 pages
File Size : 50,8 Mb
Release : 2015-11-30
Category : Technology & Engineering
ISBN : 9781119078852

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Pattern Recognition in Computational Molecular Biology by Mourad Elloumi,Costas Iliopoulos,Jason T. L. Wang,Albert Y. Zomaya Pdf

A comprehensive overview of high-performance pattern recognition techniques and approaches to Computational Molecular Biology This book surveys the developments of techniques and approaches on pattern recognition related to Computational Molecular Biology. Providing a broad coverage of the field, the authors cover fundamental and technical information on these techniques and approaches, as well as discussing their related problems. The text consists of twenty nine chapters, organized into seven parts: Pattern Recognition in Sequences, Pattern Recognition in Secondary Structures, Pattern Recognition in Tertiary Structures, Pattern Recognition in Quaternary Structures, Pattern Recognition in Microarrays, Pattern Recognition in Phylogenetic Trees, and Pattern Recognition in Biological Networks. Surveys the development of techniques and approaches on pattern recognition in biomolecular data Discusses pattern recognition in primary, secondary, tertiary and quaternary structures, as well as microarrays, phylogenetic trees and biological networks Includes case studies and examples to further illustrate the concepts discussed in the book Pattern Recognition in Computational Molecular Biology: Techniques and Approaches is a reference for practitioners and professional researches in Computer Science, Life Science, and Mathematics. This book also serves as a supplementary reading for graduate students and young researches interested in Computational Molecular Biology.