Computing For Comparative Microbial Genomics

Author : David Wayne Ussery
Publisher : Springer Science & Business Media
ISBN 13 : 1848002548
Total Pages : 272 pages
Book Rating : 4.48/5 ( download)

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Download or read book Computing for Comparative Microbial Genomics written by David Wayne Ussery and published by Springer Science & Business Media. This book was released on 2009-02-26 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Author : Eugene V. Koonin
Publisher : Springer Science & Business Media
ISBN 13 : 1475737831
Total Pages : 482 pages
Book Rating : 4.37/5 ( download)

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Download or read book Sequence — Evolution — Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Ying Xu
Publisher : World Scientific
ISBN 13 : 1860949827
Total Pages : 494 pages
Book Rating : 4.21/5 ( download)

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Download or read book Computational Methods for Understanding Bacterial and Archaeal Genomes written by Ying Xu and published by World Scientific. This book was released on 2008 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Author : Mohammed Kuddus
Publisher : Frontiers Media SA
ISBN 13 : 2889746259
Total Pages : 127 pages
Book Rating : 4.55/5 ( download)

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Download or read book Computational Genomics and structural Bioinformatics in Microbial Science written by Mohammed Kuddus and published by Frontiers Media SA. This book was released on 2022-03-09 with total page 127 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Author : Arcady R. Mushegian
Publisher : Elsevier
ISBN 13 : 9780080546094
Total Pages : 280 pages
Book Rating : 4.99/5 ( download)

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Download or read book Foundations of Comparative Genomics written by Arcady R. Mushegian and published by Elsevier. This book was released on 2010-07-20 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Author : Francesca D. Ciccarelli
Publisher : Springer
ISBN 13 : 3642047440
Total Pages : 249 pages
Book Rating : 4.42/5 ( download)

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Download or read book Comparative Genomics written by Francesca D. Ciccarelli and published by Springer. This book was released on 2009-09-30 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: As genome-sequencing costs continue their downward spiral, sequencing of closely related organisms has become increasingly a?ordable. The growing amount of genomic data available demands for the constant development of computational tools to be applied in comparative genomics. The RECOMB Workshop on C- parative Genomics (RECOMB-CG) is devoted to bringing together scientists working on all aspects of comparative genomics, from computer scientists, ma- ematicians and statisticians working on novel computational approaches for genome analysis and comparison, to biologists applying these computational tools to study the structure and the evolution of prokaryotic and eukaryotic genomes. This volume contains the 19 papers presented at the 7th Annual RECOMB-CG workshop held during September 27–29, 2009 at the Renyi Institute, in Budapest, Hungary. The papers published in these proceedings were selected for oral p- sentation from 31 submissions from scientists around the world. Each paper was reviewed by at least three members of the Program Committee in a stringent and thoughtful peer-review process.

Author : Jens Lagergren
Publisher : Springer Science & Business Media
ISBN 13 : 3540244557
Total Pages : 139 pages
Book Rating : 4.54/5 ( download)

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Download or read book Comparative Genomics written by Jens Lagergren and published by Springer Science & Business Media. This book was released on 2005-03-01 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-proceedings of the RECOMB 2004 Satellite Workshop on Comparative Genomics, RCG 2004, held in Bertinoro, Italy in October 2004. The 10 revised full papers presented were carefully reviewed and improved for inclusion in the book. The papers address a broad variety of aspects of comparative genomics ranging from new quantitative discoveries about genome structures and processes to theorems on the complexity of computational problems inspired by genome comparison.

Author : Glenn Tesler
Publisher : Springer Science & Business Media
ISBN 13 : 3540749594
Total Pages : 203 pages
Book Rating : 4.92/5 ( download)

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Download or read book Comparative Genomics written by Glenn Tesler and published by Springer Science & Business Media. This book was released on 2007-08-31 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2007, held in San Diego, CA, USA, in September 2007. The 14 revised full papers presented address a broad variety of aspects and components of the field of comparative genomics, ranging from quantitative discoveries about genome structure to algorithms for comparative inference to theorems on the complexity of computational problems required for genome comparison.

Author : Zhong Wang
Publisher : World Scientific
ISBN 13 : 9811242488
Total Pages : 210 pages
Book Rating : 4.89/5 ( download)

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Download or read book Introduction To Computational Metagenomics written by Zhong Wang and published by World Scientific. This book was released on 2022-04-11 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Breakthroughs in high-throughput genome sequencing and high-performance computing technologies have empowered scientists to decode many genomes including our own. Now they have a bigger ambition: to fully understand the vast diversity of microbial communities within us and around us, and to exploit their potential for the improvement of our health and environment. In this new field called metagenomics, microbial genomes are sequenced directly from the habitats without lab cultivation. Computational metagenomics, however, faces both a data challenge that deals with tens of tera-bases of sequences and an algorithmic one that deals with the complexity of thousands of species and their interactions.This interdisciplinary book is essential reading for those who are interested in beginning their own journey in computational metagenomics. It is a prism to look through various intricate computational metagenomics problems and unravel their three distinctive aspects: metagenomics, data engineering, and algorithms. Graduate students and advanced undergraduates from genomics science or computer science fields will find that the concepts explained in this book can serve as stepping stones for more advanced topics, while metagenomics practitioners and researchers from similar disciplines may use it to broaden their knowledge or identify new research targets.

Author : Francesca D. Ciccarelli
Publisher : Springer
ISBN 13 : 9783642047459
Total Pages : 241 pages
Book Rating : 4.59/5 ( download)

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Download or read book Comparative Genomics written by Francesca D. Ciccarelli and published by Springer. This book was released on 2009-10-12 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: As genome-sequencing costs continue their downward spiral, sequencing of closely related organisms has become increasingly a?ordable. The growing amount of genomic data available demands for the constant development of computational tools to be applied in comparative genomics. The RECOMB Workshop on C- parative Genomics (RECOMB-CG) is devoted to bringing together scientists working on all aspects of comparative genomics, from computer scientists, ma- ematicians and statisticians working on novel computational approaches for genome analysis and comparison, to biologists applying these computational tools to study the structure and the evolution of prokaryotic and eukaryotic genomes. This volume contains the 19 papers presented at the 7th Annual RECOMB-CG workshop held during September 27–29, 2009 at the Renyi Institute, in Budapest, Hungary. The papers published in these proceedings were selected for oral p- sentation from 31 submissions from scientists around the world. Each paper was reviewed by at least three members of the Program Committee in a stringent and thoughtful peer-review process.