Comparative Genomics

This second edition provides new and updated chapters covering computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those that address general techniques and concepts that apply to all organisms to others that are specialized and apply to specific biological systems such as viruses, bacteria, nematodes, and insects. Well-known comparative genomics web-based platforms are also covered in specific chapters. Written in the highly successful Methods in Molecular Biology series format, many chapters include introductions to their respective topics and step-by-step comparison procedures, demonstrated on actual sets of genome sequences. Authoritative and cutting-edge, Comparative Genomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

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.

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel. The volume is intended for molecular biologists, biochemists and geneticists.

When genomic research first came on the scene, much of the biomedical research community viewed it as a limited venture with limited potential. We now know that such an assessment was both highly premature and wonderfully inaccurate. In the last ten years, we’ve witnessed such remarkable acceleration in the merger of basic and applied genomic research that, among other things, genomic research is now thought of as being intrinsic to current drug research. Through rigorous comparative analysis, the genomes of cold-blooded vertebrate, avian, and other mammalian species are providing a deeper understanding of the human genome. Moreover, genomic sequences, which are becoming available for several species have proven to be highly relevant to drug research with regard to a number of otherwise intractable conditions. Rather than offering a comprehensive volume covering every aspect of comparative genomics, Comparative Genomics: Basic and Applied Research embodies the diverse interests of prominent researchers in the field. Compiling first hand descriptions of their pioneering work, the text focuses on commonalities and synergies across the broad field of comparative genomics. Among its many topics it covers— · Revolutionary advances in DNA-sequencing technology · Bold new approaches to the organization and analysis of large phylogenetic data sets · The impact of comparative genomics on our understanding of evolution · Efforts toward developing novel antimicrobial drugs, through the use of bacterial pathogen genomes Ultimately, future breakthroughs in comparative genomics will depend upon the continued interaction and interdependency of applied and basic research. This seminal volume demonstrates both the means and the fruits of that cooperation, and in doing so defines and lays the groundwork for continued progress.

This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.

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

This comprehensive reference covers the comparative methodology involved in studying molecular evolution. Providing a practical introduction to the role of bioinformatics in comparative genomics, this publication further discusses the basic technology used in genome sequencing projects and provides an overview of genome storage databases currently in use. This timely and cutting-edge text also: * Reviews the basic principles of genomics and gene expression analysis * Discusses analytic methods in proteomics and transcriptomics * Includes a comprehensive list of Web resource

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel. The volume is intended for molecular biologists, biochemists and geneticists.