Computer Analysis Of Sequence Data

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Computer Analysis Of Sequence Data Part I

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Author : Annette M. Griffin
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-02

Computer Analysis Of Sequence Data Part I written by Annette M. Griffin 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 2008-02-02 with Science categories.

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gen- ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods ess- tial to analysis, and a familiarity with computers and sequence ana- sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Analysis of Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or p- tein) sequences. Each chapter is written such that a competent sci- tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed pr- tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes enco- tered by users of the sequence analysis software. Software packages for both the mainframe and personal computers are described.

Computer Analysis Of Sequence Data Part Ii

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Author : Annette M. Griffin
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-02

Computer Analysis Of Sequence Data Part Ii written by Annette M. Griffin 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 2008-02-02 with Science categories.

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gener ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods essen tial to analysis, and a familiarity with computers and sequence analy sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Computer Analysis of Sequence Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or pro tein) sequences. Each chapter is written such that a competent scien tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed prac tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes encoun tered by users of the sequence analysis software.

Biological Sequence Analysis

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Author : Richard Durbin
language : en
Publisher: Cambridge University Press
Release Date : 1998-04-23

Biological Sequence Analysis written by Richard Durbin and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998-04-23 with Medical categories.

Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

Sequence Data Mining

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Author : Guozhu Dong
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-10-31

Sequence Data Mining written by Guozhu Dong 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 2007-10-31 with Computers categories.

Understanding sequence data, and the ability to utilize this hidden knowledge, will create a significant impact on many aspects of our society. Examples of sequence data include DNA, protein, customer purchase history, web surfing history, and more. This book provides thorough coverage of the existing results on sequence data mining as well as pattern types and associated pattern mining methods. It offers balanced coverage on data mining and sequence data analysis, allowing readers to access the state-of-the-art results in one place.

Computer Analysis Of Sequence Data

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Author : Annette M. Griffin
language : en
Publisher:
Release Date :

Computer Analysis Of Sequence Data written by Annette M. Griffin and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on with Amino acid sequence categories.

Guide To Human Genome Computing

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Author : Martin J. Bishop
language : en
Publisher: Academic Press
Release Date : 1998-03-25

Guide To Human Genome Computing written by Martin J. Bishop and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998-03-25 with Science categories.

The Guide to Human Genome Computing is invaluable to scientists who wish to make use of the powerful computing tools now available to assist them in the field of human genome analysis. This book clearly explains access and use of sequence databases, and presents the various computer packages used to analyze DNA sequences, measure linkage analysis, compare and align DNA sequences from different genes or organisms, and infer structural and functional information about proteins from sequence data. This Second Edition contains completely updated material. Rather than a revision of the previous volume, the Second Edition is essentially a new book, based on the subjects which will be of interest over the coming years. This new book is international, both in scope and authorship. - Computing resources for the following are clearly explained: Internet resources - databases etc. - Genetic analysis - Sib-pair studies - Comparative mapping - Radiation hybrids - Sequence ready clone maps - Human genome sequencing - ESTs - Gene prediction - Gene expression

Mapping And Sequencing The Human Genome

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Author : National Research Council
language : en
Publisher: National Academies Press
Release Date : 1988-01-01

Mapping And Sequencing The Human Genome 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 1988-01-01 with Science categories.

There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a monumental project that will have far-reaching consequences for medicine, biology, technology, and other fields. But how will such an effort be organized and funded? How will we develop the new technologies that are needed? What new legal, social, and ethical questions will be raised? Mapping and Sequencing the Human Genome is a blueprint for this proposed project. The authors offer a highly readable explanation of the technical aspects of genetic mapping and sequencing, and they recommend specific interim and long-range research goals, organizational strategies, and funding levels. They also outline some of the legal and social questions that might arise and urge their early consideration by policymakers.

Computational Genomics With R

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Author : Altuna Akalin
language : en
Publisher: CRC Press
Release Date : 2020-12-16

Computational Genomics With R written by Altuna Akalin and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-12-16 with Mathematics categories.

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.

Computational Methods For Next Generation Sequencing Data Analysis

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Author : Ion Mandoiu
language : en
Publisher: John Wiley & Sons
Release Date : 2016-10-03

Computational Methods For Next Generation Sequencing Data Analysis written by Ion Mandoiu 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 2016-10-03 with Computers categories.

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.

Encyclopedia Of Bioinformatics And Computational Biology

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Author : Christian Schönbach
language : en
Publisher:
Release Date : 2018

Encyclopedia Of Bioinformatics And Computational Biology written by Christian Schönbach and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.