Next Generation Sequencing Technologies And Challenges In Sequence Assembly

Author : Sara El-Metwally,Osama M. Ouda,Mohamed Helmy
Publisher : Springer Science & Business
Page : 118 pages
File Size : 43,5 Mb
Release : 2014-04-19
Category : Science
ISBN : 9781493907151

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Next Generation Sequencing Technologies and Challenges in Sequence Assembly by Sara El-Metwally,Osama M. Ouda,Mohamed Helmy Pdf

The introduction of Next Generation Sequencing (NGS) technologies resulted in a major transformation in the way scientists extract genetic information from biological systems, revealing limitless insight about the genome, transcriptome and epigenome of any species. However, with NGS, came its own challenges that require continuous development in the sequencing technologies and bioinformatics analysis of the resultant raw data and assembly of the full length genome and transcriptome. Such developments lead to outstanding improvements of the performance and coverage of sequencing and improved quality for the assembled sequences, nevertheless, challenges such as sequencing errors, expensive processing and memory usage for assembly and sequencer specific errors remains major challenges in the field. This book aims to provide brief overviews the NGS field with special focus on the challenges facing the NGS field, including information on different experimental platforms, assembly algorithms and software tools, assembly error correction approaches and the correlated challenges.

Author : M. Sc Sara El-Metwally,Osama M. Ouda,Mohamed Helmy
Publisher : Unknown
Page : 132 pages
File Size : 50,7 Mb
Release : 2014-05-31
Category : Electronic
ISBN : 1493907166

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Next Generation Sequencing Technologies and Challenges in Sequence Assembly by M. Sc Sara El-Metwally,Osama M. Ouda,Mohamed Helmy Pdf

Author : Jerzy Kulski
Publisher : BoD – Books on Demand
Page : 466 pages
File Size : 41,9 Mb
Release : 2016-01-14
Category : Medical
ISBN : 9789535122401

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Next Generation Sequencing by Jerzy Kulski Pdf

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.

Author : Ali Masoudi-Nejad,Zahra Narimani,Nazanin Hosseinkhan
Publisher : Springer Science & Business Media
Page : 86 pages
File Size : 43,8 Mb
Release : 2013-07-09
Category : Medical
ISBN : 9781461477266

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Next Generation Sequencing and Sequence Assembly by Ali Masoudi-Nejad,Zahra Narimani,Nazanin Hosseinkhan Pdf

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 : Kuo Ping Chiu
Publisher : Bentham Science Publishers
Page : 160 pages
File Size : 55,6 Mb
Release : 2015-11-04
Category : Science
ISBN : 9781681080925

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Next-Generation Sequencing and Sequence Data Analysis by Kuo Ping Chiu Pdf

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 : Ion Mandoiu,Alexander Zelikovsky
Publisher : John Wiley & Sons
Page : 464 pages
File Size : 53,5 Mb
Release : 2016-09-12
Category : Computers
ISBN : 9781119272168

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Computational Methods for Next Generation Sequencing Data Analysis by Ion Mandoiu,Alexander Zelikovsky Pdf

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 : Sun Kim
Publisher : Artech House Publishers
Page : 288 pages
File Size : 46,7 Mb
Release : 2008
Category : Computers
ISBN : STANFORD:36105124046231

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Genome Sequencing Technology and Algorithms by Sun Kim Pdf

The 2003 completion of the Human Genome Project was just one step in the evolution of DNA sequencing. This trailblazing work gives researchers unparalleled access to state-of-the-art DNA sequencing technologies, new algorithmic sequence assembly techniques, and emerging methods for both resequencing and genome analysis.

Author : Durgesh Kumar Tripathi,Vijay Pratap Singh,Devendra Kumar Chauhan,Shivesh Sharma,Sheo Mohan Prasad,Nawal Kishore Dubey,Naleeni Ramawat
Publisher : Academic Press
Page : 1014 pages
File Size : 45,7 Mb
Release : 2020-04-10
Category : Science
ISBN : 9780128182055

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Plant Life under Changing Environment by Durgesh Kumar Tripathi,Vijay Pratap Singh,Devendra Kumar Chauhan,Shivesh Sharma,Sheo Mohan Prasad,Nawal Kishore Dubey,Naleeni Ramawat Pdf

Plant Life under Changing Environment: Responses and Management presents the latest insights, reflecting the significant progress that has been made in understanding plant responses to various changing environmental impacts, as well as strategies for alleviating their adverse effects, including abiotic stresses. Growing from a focus on plants and their ability to respond, adapt, and survive, Plant Life under Changing Environment: Responses and Management addresses options for mitigating those responses to ensure maximum health and growth. Researchers and advanced students in environmental sciences, plant ecophysiology, biochemistry, molecular biology, nano-pollution climate change, and soil pollution will find this an important foundational resource. Covers both responses and adaptation of plants to altered environmental states Illustrates the current impact of climate change on plant productivity, along with mitigation strategies Includes transcriptomic, proteomic, metabolomic and ionomic approaches

Author : Jagajjit Sahu,Anukool Vaishnav,Harikesh Bahadur Singh
Publisher : CRC Press
Page : 324 pages
File Size : 50,9 Mb
Release : 2022-07-28
Category : Medical
ISBN : 9781000613940

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Plant-Microbe Interactions by Jagajjit Sahu,Anukool Vaishnav,Harikesh Bahadur Singh Pdf

A constant research effort to understand plant-microbe interactions makes it indispensable to keep abreast of the latest research developments. Researchers from a range of disciplines have used multiple approaches to infer this field. With the advent of next-generation techniques, both molecular and computational, the field has entered a new phase. These approaches often result in massive information, which is sometimes tangled and in need of further analysis. These types of analyses also require cutting-edge data analytics as well as efficient statistical models. Plant-Microbe Interactions: Harnessing Next-Generation Molecular Technologies for Sustainable Agriculture provides a comprehensive picture of the modern-day analytics and approaches being used to provide insights into the interactions between plant and microbe. A wide range of technologies are explored along with practical guides toward these techniques. A detailed understanding of omics data in various areas could be obtained from this compilation. Key Features: • Crosstalk between plant and microbe • Overview of advanced molecular techniques used to study plant-microbe interaction • Practical guide to technologies such as NGS • Omics data analysis used to study plant-microbe interaction • Role of soil metagenomics • Advanced technologies such as nanotechnology and CRISPR serving to study plant-microbe interaction This book will serve as a great reference to various next-generation techniques in the field of plant-microbe interaction, thereby helping to better understand the mechanism. This will also help budding researchers to shape their research in similar areas.

Author : Ray Ming
Publisher : Springer
Page : 281 pages
File Size : 49,6 Mb
Release : 2018-11-27
Category : Science
ISBN : 9783030006143

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Genetics and Genomics of Pineapple by Ray Ming Pdf

This book is the first comprehensive volume on the genetics and genomics of pineapple and provides an overview of the current state of pineapple research. Pineapple [Ananas comosus (L.) Merr.] is the second most important tropical fruit after banana in term of international trade. Its features are advantageous for genomic research: it has a small genome of 527 Mb which is diploid and vegetatively propagated; it is monocot, closely related to the grass family that includes major cereal crops, wheat, rice, corn, sorghum, and millet; and it serves as an out group for genetic and genomic research in grasses. In addition to exploring the evolution and improvement of pineapple, this work examines the pineapple genome with respect to genome structure and organization, comparative analyses with other angiosperm genomes, transcription factors, disease resistance, and circadian clock regulation of CAM related genes. With chapters covering botanical, genetic, genomic, and applied aspects of pineapple, this text also encourages the application of genomic technologies and suggests future prospects.

Author : C. Alexander Valencia,M. Ali Pervaiz,Ammar Husami,Yaping Qian,Kejian Zhang
Publisher : Springer Science & Business Media
Page : 94 pages
File Size : 40,7 Mb
Release : 2013-10-16
Category : Medical
ISBN : 9781461490326

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Next Generation Sequencing Technologies in Medical Genetics by C. Alexander Valencia,M. Ali Pervaiz,Ammar Husami,Yaping Qian,Kejian Zhang Pdf

This book introduces readers to Next Generation Sequencing applications in medical genetics. The authors discuss the direct application of next-generation sequencing to medicine, specifically, laboratory medicine or molecular diagnostics. The first part of the book contains chapters on sanger sequencing, NGS technologies, targeted-amplification and capture, and exome sequencing. The second part of the book focuses on genetic disorders diagnoses by NGS, prenatal diagnosis, muscular dystrophies, mitochondrial disorders diagnosis, and challenges in molecular diagnosis. Recent developments and potential future trends in NGS sequencing applications are highlighted, as well.​

Author : Xinkun Wang
Publisher : CRC Press
Page : 258 pages
File Size : 42,7 Mb
Release : 2016-04-06
Category : Mathematics
ISBN : 9781482217896

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Next-Generation Sequencing Data Analysis by Xinkun Wang Pdf

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

Author : Keith R. Mitchelson
Publisher : Elsevier
Page : 398 pages
File Size : 54,5 Mb
Release : 2011-09-22
Category : Science
ISBN : 0080471285

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New High Throughput Technologies for DNA Sequencing and Genomics by Keith R. Mitchelson Pdf

Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century. Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book. * 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine. * Bringing together new developments in DNA sequencing technology * Reviewing issues relevant to the new applications used

Author : Andreas Sundquist
Publisher : Unknown
Page : 118 pages
File Size : 45,5 Mb
Release : 2008
Category : Electronic
ISBN : STANFORD:36105210223975

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Algorithms for Next-generation Sequencing by Andreas Sundquist Pdf

Author : RC Sobti,Manishi Mukesh,Aastha Sobti
Publisher : CRC Press
Page : 420 pages
File Size : 45,7 Mb
Release : 2022-12-29
Category : Medical
ISBN : 9781000782561

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Genomic, Proteomics, and Biotechnology by RC Sobti,Manishi Mukesh,Aastha Sobti Pdf

High-throughput molecular technologies ("omics") can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways thereby allowing the discovery of biomarkers. Notably, the omics technologies along with and computational methods, bioprospecting, and artificial intelligence will continue to lead to better understanding of biological mechanisms that are responsible for physical attributes, or phenotypes. Research breakthroughs obtained through these technologies can be used to enhance productivity of food animals, meet the increasing demand for animal-sourced foods, enhance high-quality nutrient availability, ensure nutrient safety, mitigate the effects of climate variability, and result in new technologies that provide continued improvement in food security worldwide. Such breakthroughs are an urgent necessity because over the past 50 years, there has been an unprecedented increase in the world’s population, which will reach ten billion by the year 2050. Innovative and technological advancements that enhance all aspects of food production will arise from basic, fundamental research. Besides food, animal by-products have found many applications in the fields of pharmaceuticals, cosmetics, and household and industrial products. Hence, the need to ameliorate the productivity, reproductivity, growth performance, and disease resistance in animals has created a worldwide interest in gaining a deeper understanding of animal biology, biotechnology and genomics, and proteomics. The present volume thoroughly discusses the omics studies in domestic and non-domestic animals and their role in mitigation of various challenges ahead. The volume thus focuses on i. Omics (genomics, proteomics, transcriptomics, metabolonomics) technologies in identifying, characterizing biodiversity ii. Role of molecular techniques for improvement of domestic and non-domestic organisms iii. Animal and alternative model systems (using stem cells, tissue engineering, cell free systems, 3D platforms etc.) for studying life phenomena iv. Genetically modified organisms as factories for the products