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Author: Anna Blomstergren
Publisher:
ISBN: 9789172836082
Category :
Languages : en
Pages : 72
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Book Description
Author: Anna Blomstergren
Publisher:
ISBN: 9789172836082
Category :
Languages : en
Pages : 72
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Book Description
Author: Ion Mandoiu
Publisher: John Wiley & Sons
ISBN: 1119272165
Category : Computers
Languages : en
Pages : 464
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Book Description
Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.
Author: Ali Masoudi-Nejad
Publisher: Springer Science & Business Media
ISBN: 1461477263
Category : Medical
Languages : en
Pages : 92
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Book Description
The goal of this book is to introduce the biological and technical aspects of next generation sequencing methods, as well as algorithms to assemble these sequences into whole genomes. The book is organized into two parts; part 1 introduces NGS methods and part 2 reviews assembly algorithms and gives a good insight to these methods for readers new to the field. Gathering information, about sequencing and assembly methods together, helps both biologists and computer scientists to get a clear idea about the field. Chapters will include information about new sequencing technologies such as ChIp-seq, ChIp-chip, and De Novo sequence assembly.
Author: Applied Research Press
Publisher: Createspace Independent Publishing Platform
ISBN: 9781515216209
Category :
Languages : en
Pages : 42
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Book Description
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.
Author: Stéphane Deschamps
Publisher:
ISBN:
Category : Science
Languages : en
Pages :
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Book Description
The field of plant genome assembly has greatly benefited from the development and widespread adoption of next-generation DNA sequencing platforms. Very high sequencing throughputs and low costs per nucleotide have considerably reduced the technical and budgetary constraints associated with early assembly projects done primarily with a traditional Sanger-based approach. Those improvements led to a sharp increase in the number of plant genomes being sequenced, including large and complex genomes of economically important crops. Although next-generation DNA sequencing has considerably improved our understanding of the overall structure and dynamics of many plant genomes, severe limitations still remain because next-generation DNA sequencing reads typically are shorter than Sanger reads. In addition, the software tools used to de novo assemble sequences are not necessarily designed to optimize the use of short reads. These cause challenges, common to many plant species with large genome sizes, high repeat contents, polyploidy and genome-wide duplications. This chapter provides an overview of historical and current methods used to sequence and assemble plant genomes, along with new solutions offered by the emergence of technologies such as single molecule sequencing and optical mapping to address the limitations of current sequence assemblies.
Author: Kuo Ping Chiu
Publisher: Bentham Science Publishers
ISBN: 1681080923
Category : Science
Languages : en
Pages : 160
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Book Description
Nucleic acid sequencing techniques have enabled researchers to determine the exact order of base pairs - and by extension, the information present - in the genome of living organisms. Consequently, our understanding of this information and its link to genetic expression at molecular and cellular levels has lead to rapid advances in biology, genetics, biotechnology and medicine. Next-Generation Sequencing and Sequence Data Analysis is a brief primer on DNA sequencing techniques and methods used to analyze sequence data. Readers will learn about recent concepts and methods in genomics such as sequence library preparation, cluster generation for PCR technologies, PED sequencing, genome assembly, exome sequencing, transcriptomics and more. This book serves as a textbook for students undertaking courses in bioinformatics and laboratory methods in applied biology. General readers interested in learning about DNA sequencing techniques may also benefit from the simple format of information presented in the book.
Author: Nils Stein
Publisher: Springer
ISBN: 3319925288
Category : Science
Languages : en
Pages : 400
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Book Description
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.
Author: Ibrokhim Y. Abdurakhmonov
Publisher: BoD – Books on Demand
ISBN: 1789232686
Category : Medical
Languages : en
Pages : 190
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Book Description
Bioinformatics has evolved significantly in the era of post genomics and big data. Huge advancements were made toward storing, handling, mining, comparing, extracting, clustering and analysis as well as visualization of big macromolecular data using novel computational approaches, machine and deep learning methods, and web-based server tools. There are extensively ongoing world-wide efforts to build the resources for regional hosting, organized and structured access and improving the pre-existing bioinformatics tools to efficiently and meaningfully analyze day-to-day increasing big data. This book intends to provide the reader with updates and progress on genomic data analysis, data modeling and network-based system tools.
Author: Wilhelm Ansorge
Publisher: Wiley-Liss
ISBN:
Category : Medical
Languages : en
Pages : 220
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Book Description
This outstanding lab bench reference to the technology of DNA sequencing offers a collection of concise sequencing strategies and cloning protocols. Concentrates on the most up-to-the-minute automated methods and advanced approaches. Preparing DNA for sequencing, sequencing single- doubled-stranded DNA and their variations, how to optimise the primers used, preparation of DNA sequencing gels and the actual collection of results, labelling of DNA fragments for sequencing and data analysis are among the topics covered.
Author: Matthew Pendleton
Publisher:
ISBN:
Category :
Languages : en
Pages : 163
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Book Description
In the post-human genome era we have amassed endless genome sequencing data, but our ability to address variation between genomes has been largely restricted to small indels and single nucleotide variations. More complex regions of the genome, such as highly repetitive regions or those containing structural variation, have been largely ignored. This proposal aims to help elucidate these regions via a combination of computational and experimental approaches.First, we seek to build computational tools for identifying and computing large genomic differences by taking advantage of “third-generation” DNA sequencing technologies. This is done, in part, using a novel structural variation tool which uses a systematic framework for interrogating sequence “dot plots” (or groups of sequence “dot plots”) which have been historically used for visual identification of genome rearrangements, especially for complex comparative genomics. We combine these approaches with established tools for identifying single nucleotide variations (SNVs), to calculate multi-event co-variance in two constrained cancer projects: HCV viral quasispecies analysis in liver cancer, and FLT3 tyrosine kinase variation in acute myelogenous leukemia (AML). We then apply and extend these methods (along with existing methods for assembly, scaffolding, and phasing) in the context of the first amplification-free, diploid human genome assembly. In addition to enumerating far more structural variation than has been previously seen, this work provides the first human assembly that combines single molecule real time sequencing on Pacific BioSciences’ SMRT RT II sequencing platform with optical mapping generated by BioNano Genomics Irys mapping system. This hybrid strategy results in a de novo assembled genome that approaches reference quality.Second, to target the most complicated regions of the genome, we propose a pair of new amplification-free enrichment technologies. One approach combines an old mainstay of human genomics, the pulsed field gel electrophoresis, with the power of RNA guided cas9 endonuclease to enable enrichment of high molecular weight DNA from genome intervals that are difficult to manipulate with BAC cloning methods. The other approach employs an inactivated Cas9 protein engineered to permit bead based pull-down of a targeted region. We believe these approaches fill-in a needed gap, where resolution of structural variants, unambiguous haplotypic resolution and complete assembly would be impossible with existing targeting approaches but prohibitively expensive using high depth, long read whole genome sequencing.
