An Approach To Improved Microbial Eukaryotic Genome Annotation
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An Approach To Improved Microbial Eukaryotic Genome Annotation
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Author : Matthew Sarrasin
language : en
Publisher:
Release Date : 2017
An Approach To Improved Microbial Eukaryotic Genome Annotation written by Matthew Sarrasin and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
New sequencing technologies have considerably accelerated the rate at which genomic data is being generated. One ongoing challenge is the accurate structural annotation of those novel genomes once sequenced and assembled, in particular if the organism does not have close relatives with well-annotated genomes. Whole-transcriptome sequencing (RNA-Seq) and assembly-both of which share similarities to whole-genome sequencing and assembly, respectively-have been shown to dramatically increase the accuracy of gene annotation. Read coverage, inferred splice junctions and assembled transcripts can provide valuable information about gene structure. Several annotation pipelines have been developed to automate structural annotation by incorporating information from RNA-Seq, as well as protein sequence similarity data, with the goal of reaching the accuracy of an expert curator. Annotation pipelines follow a similar workflow. The first step is to identify repetitive regions to prevent misinformed sequence alignments and gene predictions. The next step is to construct a database of evidence from experimental data such as RNA-Seq mapping and assembly, and protein sequence alignments, which are used to inform the generalised Hidden Markov Models of gene prediction software. The final step is to consolidate sequence alignments and gene predictions into a high-confidence consensus set. Thus, automated pipelines are complex, and therefore susceptible to incomplete and erroneous use of information, which can poison gene predictions and consensus model building. Here, we present an improved approach to microbial eukaryotic genome annotation. Its conception was based on identifying and mitigating potential sources of error and bias that are present in available pipelines. Our approach has two main aspects. The first is to create a more complete and diverse set of extrinsic evidence to better inform gene predictions. The second is to use extrinsic evidence in tandem with predictions such that the influence of their respective biases in the consensus gene models is reduced. We benchmarked our new tool against three known pipelines, showing significant gains in gene, transcript, exon and intron sensitivity and specificity in the genome annotation of microbial eukaryotes.
Sequence Evolution Function
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Author : Eugene V. Koonin
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-06-29
Sequence Evolution Function written by Eugene V. Koonin and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-06-29 with Science categories.
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.
The Pangenome
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Author : Hervé Tettelin
language : en
Publisher: Springer Nature
Release Date : 2020-04-30
The Pangenome written by Hervé Tettelin and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-04-30 with Science categories.
This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Long Non Coding Rna Biology
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Author : M.R.S. Rao
language : en
Publisher: Springer
Release Date : 2017-08-16
Long Non Coding Rna Biology written by M.R.S. Rao and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-08-16 with Medical categories.
This contributed volume offers a comprehensive and detailed overview of the various aspects of long non-coding RNAs and discusses their emerging significance. Written by leading experts in the field, it motivates young researchers around the globe, and offers graduate and postgraduate students fascinating insights into genes and their regulation in eukaryotes and higher organisms.
The New Science Of Metagenomics
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Author : National Research Council
language : en
Publisher: National Academies Press
Release Date : 2007-06-24
The New Science Of Metagenomics written by National Research Council and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-06-24 with Science categories.
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Functional Metagenomics Tools And Applications
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Author : Trevor C. Charles
language : en
Publisher: Springer
Release Date : 2017-10-09
Functional Metagenomics Tools And Applications written by Trevor C. Charles and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-09 with Science categories.
In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
Pan Genomics Applications Challenges And Future Prospects
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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2020-03-06
Pan Genomics Applications Challenges And Future Prospects written by Debmalya Barh and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-06 with Science categories.
Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, “case studies in pan-genomics, thoroughly discusses twelve case, and the last, “current approaches and future prospects in pan-multiomics , encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives Discusses current bioinformatics tools and strategies for exploiting pangenomics data Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability
Microbiome In Human Health And Disease
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Author : Pallaval Veera Bramhachari
language : en
Publisher: Springer Nature
Release Date : 2021-10-18
Microbiome In Human Health And Disease written by Pallaval Veera Bramhachari and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-18 with Medical categories.
The book provides an overview on how the microbiome contributes to human health and disease. The microbiome has also become a burgeoning field of research in medicine, agriculture & environment. The readers will obtain profound knowledge on the connection between intestinal microbiota and immune defense systems, medicine, agriculture & environment. The book may address several researchers, clinicians and scholars working in biomedicine, microbiology and immunology. The application of new technologies has no doubt revolutionized the research initiatives providing new insights into the dynamics of these complex microbial communities and their role in medicine, agriculture & environment shall be more emphasized. Drawing on broad range concepts of disciplines and model systems, this book primarily provides a conceptual framework for understanding these human-microbe, animal-microbe & plant-microbe, interactions while shedding critical light on the scientific challenges that lie ahead. Furthermore this book explains why microbiome research demands a creative and interdisciplinary thinking—the capacity to combine microbiology with human, animal and plant physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet in a typical immune system, and have contributed to animal and plant diversification over long evolutionary timescales. Also this book explains why microbiome research presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for human health and new strategies.
Gene Prediction
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Author : Martin Kollmar
language : en
Publisher: Humana Press
Release Date : 2019-05-19
Gene Prediction written by Martin Kollmar and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-05-19 with Science categories.
This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com.
Microbial Functional Genomics
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Author : Jizhong Zhou
language : en
Publisher: John Wiley & Sons
Release Date : 2004-03-19
Microbial Functional Genomics written by Jizhong Zhou and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-03-19 with Science categories.
Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.