A Tale of Three Next Generation Sequencing Platforms
A Tale of Three Next Generation Sequencing Platforms

Author: Applied Research Press

Publisher: Createspace Independent Publishing Platform

Published: 2015-07-24

Total Pages: 42

ISBN-13: 9781515216209

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Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support. Proceeds from the sale of this book go to the support of an elderly disabled person.

Flow Cytogenetics
Flow Cytogenetics

Author:

Publisher: Academic Press

Published: 2012-12-02

Total Pages: 331

ISBN-13: 0080984525

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This is the first book to be devoted entirely to the application and development of flow techniques in cytogenetics. It provides comprehensive information on the use of flow cytometry and sorting for chromosome classification and purification. Cytogenetics and molecular biologists will find this book an invaluable reference source. - Practical details for the preparation and analysis of chromosomes using flow cytometry - Flow karyotyping for sensitive rapid analysis of chromosome normality and the detection of aberrant chromosomes - Flow sorting as a source of chromosome-specific DNA for gene mapping and recombinant DNA libraries - Construction and current status of chromosome-specific recombinant DNA libraries

The Barley Genome
The Barley Genome

Author: Nils Stein

Publisher: Springer

Published: 2018-08-18

Total Pages: 400

ISBN-13: 3319925288

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This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.

Next Generation Sequencing
Next Generation Sequencing

Author: Jerzy Kulski

Publisher: BoD – Books on Demand

Published: 2016-01-14

Total Pages: 466

ISBN-13: 9535122401

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Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Biological Sequence Analysis
Biological Sequence Analysis

Author: Richard Durbin

Publisher: Cambridge University Press

Published: 1998-04-23

Total Pages: 372

ISBN-13: 113945739X

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Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Bioinformatics for High Throughput Sequencing
Bioinformatics for High Throughput Sequencing

Author: Naiara Rodríguez-Ezpeleta

Publisher: Springer Science & Business Media

Published: 2011-10-26

Total Pages: 258

ISBN-13: 1461407826

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Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.

Flower Breeding and Genetics
Flower Breeding and Genetics

Author: Neil O. Anderson

Publisher: Springer Science & Business Media

Published: 2007-10-04

Total Pages: 860

ISBN-13: 9781402065699

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Floriculture is one of the fastest-growing sectors of commercial agriculture. This book provides a unique and valuable resource on the many issues and challenges facing flower breeders, as well as the industry at-large. Featuring contributions from 32 international authorities, it offers tools and directions for future crop domestication and enhancement as well as offers essential information for breeding a wide range of floriculture crops.

Next-Generation Sequencing Data Analysis
Next-Generation Sequencing Data Analysis

Author: Xinkun Wang

Publisher: CRC Press

Published: 2016-04-06

Total Pages: 252

ISBN-13: 1482217899

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A Practical Guide to the Highly Dynamic Area of Massively Parallel SequencingThe development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphi

Deep Sequencing Data Analysis
Deep Sequencing Data Analysis

Author: Noam Shomron

Publisher: Humana Press

Published: 2013-07-20

Total Pages: 0

ISBN-13: 9781627035132

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The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation.

The Pangenome
The Pangenome

Author: Hervé Tettelin

Publisher: Springer Nature

Published: 2020-04-30

Total Pages: 311

ISBN-13: 3030382818

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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.