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Functional Comparison Of Current Software Tools For Genomic Assembly From High Throughput Sequencing Data
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Book Synopsis Functional Comparison of Current Software Tools for Genomic Assembly from High Throughput Sequencing Data by : Lars J. Olsen
Download or read book Functional Comparison of Current Software Tools for Genomic Assembly from High Throughput Sequencing Data written by Lars J. Olsen and published by . This book was released on 2019 with total page 251 pages. Available in PDF, EPUB and Kindle. Book excerpt: "De novo genomic sequencing, which is the process of discovering the sequence of a genome which has not previously been elucidated, provides unique challenges, especially for larger genomes. Modern high-throughput sequencing technologies have addressed the issue of covering the entire genome in a reasonable time by fragmenting the genome into portions that can be examined in a massively-parallel approach. While these have saved considerable time and cost for the chemical process of determining the sequence of a genome, they result in sets of many tens of millions of sequence fragments called reads, each of which is typically on the order of just 100 to 300 bases long. Assembling these reads into a genomic sequence is highly computationally complex. A variety of assembly software packages are readily available for this purpose. In this project, a set of genomic assemblers was selected for examination. These programs were then tested with an Illumina data set for the grape species Vitis romanetii. Experimental runs with this dataset were performed to evaluate the run time required as well as the contiguity, completeness, and accuracy of the resulting assemblies. Different approaches to quality control preprocessing of the sequence data were also explored and evaluated. The results strongly recommend the use of the program MaSuRCA, run with data which has not been preprocessed for quality control. The second highest recommendation would be the use of ABySS with data preprocessed via QuorUM error-correction. In the process of these tests, it was also hoped that at least the beginnings of a draft genome for V. romanetii would be produced. The assemblies which came closest to publication quality were produced by MaSuRCA. Examination of these using the assessment software BUSCO suggest that the best of these assemblies may well be approaching publishable quality."--Abstract.
Book Synopsis Bringing Large-scale Multiple Genome Analysis One Step Closer by :
Download or read book Bringing Large-scale Multiple Genome Analysis One Step Closer written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial, viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large-scale genomics projects. The rapid growth of genome resources such as IMG cannot be sustained without more powerful tools such as ScalaBLAST that use more effectively large scale computing resources to perform the core BLAST calculations. ScalaBLAST is a high performance computing algorithm designed to give high throughput BLAST results on high-end supercomputers. Other parallel sequence comparison applications have been developed4-6. However problems with scaling generally prevent these applications from being used for very large searches. ScalaBLAST7 is the first BLAST application to be both highly scaleable against the size of the database as well as the number of computer processors on high-end hardware and on commodity clusters. ScalaBLAST achieves high throughput by parsing a large collection of query sequences into independent subgroups. These smaller tasks are assigned to independent process groups. Efficient scaling is achieved by (transparently to the user) sharing only one copy of the target database across all processors using the Global Array toolkit 8, 9, which provides software implementation of shared memory interface. ScalaBLAST was initially deployed on the 1,960 processor MPP2 cluster in the Wiliam R. Wiley Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory, and has since been ported to a variety of linux-based clusters and shared memory architectures, including SGI Altix, AMD opteron, and Intel Xeon-based clusters. Future targets include IBM BlueGene, Cray, and SGI Altix XE architectures. The importance of performing high-throughput calculations rapidly lies in the rate of growth of sequence data. For a genome sequencing center to provide multiple-genome comparison capabilities, it must keep pace with exponentially growing collection of protein data, both from its own genomes, and from the public genome information as well. As sequence data continues to grow exponentially, this challenge will only increase with time. Solving the BLAST throughput challenge for centralized data resources like IMG has the potential to unlock the power of emerging analysis methods which, until recently, were limited by the availability of multiple genome comparison data. Fig. 1 illustrates how the run-time achieved by efficient scaling in ScalaBLAST enabled the IMG all vs. all BLAST calculations to complete in roughly 1 day. Note that to keep pace with growing IMG database, we will have to double the number of processors used in these calculations during the upcoming year. Grid-based solutions for improving throughput for BLAST searches has become a popular and attractive option for some centers. The Institute for Genome Research (http://www.tigr.org/), for instance, has implemented a grid-based BLAST tool allowing users to submit requests to be farmed out to available computers on an on-demand basis.
Book Synopsis Preprocessing Algorithms and Software for Genomic Studies with High-throughput Sequencing Data by : Ilya Y. Zhbannikov
Download or read book Preprocessing Algorithms and Software for Genomic Studies with High-throughput Sequencing Data written by Ilya Y. Zhbannikov and published by . This book was released on 2015 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA sequencing technologies address problems, the solutions of which were not possible before, such as whole genome sequencing or microbial community characterization without pre-cultivation. Current High-Throughput Sequencing (HTS) techniques allow genomic studies in small labs as well as in large genomic centers. Together with modern computational software, HTS becomes a powerful tool, which allows researchers to answer important biological questions in novel ways. Despite the advantages of modern HTS technologies, large amounts of data and accompanying noise in HTS library confound bioinformatic analysis. Data preprocessing is needed in order to prepare data for subsequent analysis. Data preprocessing includes noise removal as well as techniques such as data reduction. In this dissertation I present a set of software tools that may be used in genomic studies in order to prepare HTS data for subsequent bioinformatic analysis. The first two chapters in this dissertation describe preprocessing tools developed for data denoising. In the last two chapters I explore the use of multiple genomic markers in 16S data analysis with a meta-amplicon analysis algorithm, which facilitates usage of all the information that can be obtained with 16S amplicon sequencing. Meta-amplicon analysis represents improvements on current methods used to characterize bacterial composition and community structure.
Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Exome and Genome Analysis by : Peter N. Robinson
Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
Book Synopsis CRISPR and Plant Functional Genomics by : Jen-Tsung Chen
Download or read book CRISPR and Plant Functional Genomics written by Jen-Tsung Chen and published by CRC Press. This book was released on 2024-05-08 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: CRISPR is a crucial technology in plant physiology and molecular biology resulting in more sustainable agricultural practices, including outcomes of better plant stress tolerance and crop improvement. CRISPR and Plant Functional Genomics explores ways to release the potential of plant functional genomics, one of the prevailing topics in plant biology and a critical technology for speed and precision crop breeding. This book presents achievements in plant functional genomics and features information on diverse applications using the emerging CRISPR-based genome editing technologies producing high-yield, disease-resistant, and climate-smart crops. It also includes theories on organizing strategies for upgrading the CRISPR system to increase efficiency, avoid off-target effects, and produce transgene-free edited crops. Features: Presents CRISPR-based technologies, releasing the potential of plant functional genomics Provides methods and applications of CRISPR/Cas-based plant genome editing technologies Summarizes achievements of speed and precision crop breeding using CRISPR-based technologies Illustrates strategies to upgrade the CRISPR system Supports the UN’s sustainable development goals to develop future climate-resilient crops CRISPR and Plant Functional Genomics provides extensive knowledge of CRISPR-based technologies and plant functional genomics, and is an ideal reference for researchers, graduate students, and practitioners in the field of plant sciences as well as agronomy and agriculture.
Book Synopsis Next Generation Sequencing by : Jerzy Kulski
Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Tools for the Analysis of High-throughput Genome-scale Sequence Data by : David Adrian Lopez
Download or read book Computational Tools for the Analysis of High-throughput Genome-scale Sequence Data written by David Adrian Lopez and published by . This book was released on 2016 with total page 83 pages. Available in PDF, EPUB and Kindle. Book excerpt: As high-throughput sequence data becomes increasingly used in a variety of fields, there is a growing need for computational tools that facilitate analyzing and interpreting the sequence data to extract biological meaning. To date, several computational tools have been developed to analyze raw and processed sequence data in a number of contexts. However, many of these tools primarily focus on well-studied, reference organisms, and in some cases, such as the visualization of molecular signatures in expression data, there is a scarcity or complete absence of tools. Furthermore, the compendium of genome-scale data in publicly accessible databases can be leveraged to inform new studies. The focus of this dissertation is the development of computational tools and methods to analyze high-throughput genome-scale sequence data, as well as applications in mammalian, algal, and bacterial systems. Chapter 1 introduces the challenges of analyzing high-throughput sequence data. Chapter 2 presents the Signature Visualization Tool (SaVanT), a framework to visualize molecular signatures in user-generated expression data on a sample-by-sample basis. This chapter demonstrates that SaVanT can use immune activation signatures to distinguish patients with different types of acute infections (influenza A and bacterial pneumonia), and determine the primary cell types underlying different leukemias (acute myeloid and acute lymphoblastic) and skin disorders. Chapter 3 describes the Algal Functional Annotation Tool, which biologically interprets large gene lists, such as those derived from differential expression experiments. This tool integrates data from several pathway, ontology, and protein domain databases and performs enrichment testing on gene lists for several algal genomes. Chapter 4 describes a survey of the Chlamydomonas reinhardtii transcriptome and methylome across various stages of its sexual life cycle. This chapter discusses the identification and function of 361 gamete-specific and 627 zygote-specific genes, the first base-resolution methylation map of C. reinhardtii, and the changes in chloroplast methylation throughout key stages of its life cycle. Chapter 5 presents a comparative genomics approach to identifying previously uncharacterized bacterial microcompartment (BMC) proteins. Based on genomic proximity of genes in 131 fully-sequenced bacterial genomes, this chapter describes new putative microcompartments and their function.
Author :Naiara Rodríguez-Ezpeleta Publisher :Springer Science & Business Media ISBN 13 :1461407826 Total Pages :258 pages Book Rating :4.4/5 (614 download)
Book Synopsis Bioinformatics for High Throughput Sequencing by : Naiara Rodríguez-Ezpeleta
Download or read book Bioinformatics for High Throughput Sequencing written by Naiara Rodríguez-Ezpeleta and published by Springer Science & Business Media. This book was released on 2011-10-26 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Bioinformatics by : Mahmood A. Mahdavi
Download or read book Bioinformatics written by Mahmood A. Mahdavi and published by BoD – Books on Demand. This book was released on 2011-11-02 with total page 740 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics - Trends and Methodologies is a collection of different views on most recent topics and basic concepts in bioinformatics. This book suits young researchers who seek basic fundamentals of bioinformatic skills such as data mining, data integration, sequence analysis and gene expression analysis as well as scientists who are interested in current research in computational biology and bioinformatics including next generation sequencing, transcriptional analysis and drug design. Because of the rapid development of new technologies in molecular biology, new bioinformatic techniques emerge accordingly to keep the pace of in silico development of life science. This book focuses partly on such new techniques and their applications in biomedical science. These techniques maybe useful in identification of some diseases and cellular disorders and narrow down the number of experiments required for medical diagnostic.
Book Synopsis Computational Genomics with R by : Altuna Akalin
Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Book Synopsis Clinical Molecular Diagnostics by : Shiyang Pan
Download or read book Clinical Molecular Diagnostics written by Shiyang Pan and published by Springer Nature. This book was released on 2021-07-08 with total page 889 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the discovery of molecular biomarkers, the development of laboratory testing techniques and their clinical applications, focusing on basic research to clinical practice. It introduces new and crucial knowledge and ethics of clinical molecular diagnosis. This book emphasizes the applications of clinical molecular diagnostic test on health management, especially from different diseased organs. It lets readers to understand and realize precision healthcare.
Book Synopsis Virus Bioinformatics by : Manja Marz
Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.
Book Synopsis Algorithms for Massive Biological Datasets by : Douglas Wesley Bryant
Download or read book Algorithms for Massive Biological Datasets written by Douglas Wesley Bryant and published by . This book was released on 2011 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de novo and reference-guided genome assembly to gene prediction and identification, from genome annotation to gene expression, a multitude of biological questions are being asked and answered using high-throughput sequencing and computational methods. In this thesis we examine topics relating to high-throughput sequencing. Beginning with de novo assembly we outline current state-of-the-art methods for stitching short reads, the output of high-throughput sequencing experiments, into cohesive genomic contigs and scaffolds. Next we present our own de novo assembly software, QSRA, created in an effort to form longer contigs even through areas of low coverage and high error. We then present an application of short-read assembly and mutation analysis in a discussion of single nucleotide polymorphism discovery in hazelnut, followed by a review of de novo gene finding, the act of identifying genes in anonymous stretches of genomic sequence. Next we outline our supersplat software, built to align short reads generated by RNA-seq experiments, which span splice junctions, followed by the presentation of our gumby software, build to construct putative gene models from purely empirical short-read data. Finally we outline current state-of-the-art methods for discovering and quantifying alternative splicing variants from RNA-seq short-read data. High-throughput sequencing has fundamentally changed the way in which we approach biological questions. While an exceptionally powerful tool, high-throughput sequencing analysis demands equally powerful algorithmic techniques. We examine these issues through the lens of computational biology.
Book Synopsis Bioinformatics by : Dev Bukhsh Singh
Download or read book Bioinformatics written by Dev Bukhsh Singh and published by Academic Press. This book was released on 2021-10-21 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics: Methods and Applications provides a thorough and detailed description of principles, methods, and applications of bioinformatics in different areas of life sciences. It presents a compendium of many important topics of current advanced research and basic principles/approaches easily applicable to diverse research settings. The content encompasses topics such as biological databases, sequence analysis, genome assembly, RNA sequence data analysis, drug design, and structural and functional analysis of proteins. In addition, it discusses computational approaches for vaccine design, systems biology and big data analysis, and machine learning in bioinformatics.It is a valuable source for bioinformaticians, computer biologists, and members of biomedical field who needs to learn bioinformatics approaches to apply to their research and lab activities. Covers basic and more advanced developments of bioinformatics with a diverse and interdisciplinary approach to fulfill the needs of readers from different backgrounds Explains in a practical way how to decode complex biological problems using computational approaches and resources Brings case studies, real-world examples and several protocols to guide the readers with a problem-solving approach
Book Synopsis Advances in Single Molecule, Real-Time (SMRT) Sequencing by : Adam Ameur
Download or read book Advances in Single Molecule, Real-Time (SMRT) Sequencing written by Adam Ameur and published by MDPI. This book was released on 2019-11-18 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: PacBio’s single-molecule real-time (SMRT) sequencing technology offers important advantages over the short-read DNA sequencing technologies that currently dominate the market. This includes exceptionally long read lengths (20 kb or more), unparalleled consensus accuracy, and the ability to sequence native, non-amplified DNA molecules. From fungi to insects to humans, long reads are now used to create highly accurate reference genomes by de novo assembly of genomic DNA and to obtain a comprehensive view of transcriptomes through the sequencing of full-length cDNAs. Besides reducing biases, sequencing native DNA also permits the direct measurement of DNA base modifications. Therefore, SMRT sequencing has become an attractive technology in many fields, such as agriculture, basic science, and medical research. The boundaries of SMRT sequencing are continuously being pushed by developments in bioinformatics and sample preparation. This book contains a collection of articles showcasing the latest developments and the breadth of applications enabled by SMRT sequencing technology.
Book Synopsis Algorithms on Strings, Trees, and Sequences by : Dan Gusfield
Download or read book Algorithms on Strings, Trees, and Sequences written by Dan Gusfield and published by Cambridge University Press. This book was released on 1997-05-28 with total page 556 pages. Available in PDF, EPUB and Kindle. Book excerpt: String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.
