Format:
Online-Ressource (XI, 255p. 29 illus., 25 illus. in color, digital)
ISBN:
9781461407829
,
1283353407
,
9781283353403
Series Statement:
SpringerLink
Content:
The ultimate goal of bioinformatics is to extract biological knowledge out of the large amount of information generated by the scientific community. The chapters compiled in this volume will allow both biologists and computer scientists to understand the significance and potential of this discipline in the analysis of high throughput sequencing data. An essential reference book, not only for serving as guideline for the comprehension of the main data analysis steps, but also for providing new insights into existing software and inspiration to develop new applications
Content:
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 sequenc
Note:
Includes bibliographical references and index
,
Bioinformatics for High Throughput Sequencing; Preface; Contents; Contributors; Chapter 1: Introduction; 1.1 History of Genome Sequencing Technologies; 1.1.1 Sanger Sequencing and the Beginning of Bioinformatics; 1.1.2 Automated Sequencing; 1.1.3 From Single Genes to Complete Genomes: Assemblers as Critical Factors; 1.1.4 The Human Genome: The Culmination of Automated Sequencing; 1.2 Birth of a New Generation of Sequencing Technologies; 1.3 High-Throughput Sequencing Brings New Bioinformatic Challenges; 1.3.1 Specialized Requirements; 1.3.2 New Applications, New Challenges
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1.4 High-Throughput Data Analysis: Basic Steps and Specific Pipelines1.4.1 Pre-processing; 1.4.2 Detecting Modifications at the DNA Level; 1.4.3 Understanding More About RNA by Sequencing DNA; 1.4.4 Metagenomics; 1.5 What is Next?; References; Chapter 2: Overview of Sequencing Technology Platforms; 2.1 Introduction; 2.2 Genome Sequencer GS FLX; 2.2.1 Preparation of the Sequencing Library; 2.2.2 Emulsion PCR and Immobilization to Picotiter Plate; 2.2.3 Pyrosequencing; 2.3 Genome Analyzer; 2.3.1 Sequencing Library Preparation; 2.3.2 Solid Support Amplification
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2.3.3 Sequencing Using Fluorophore Labeled Reversible Terminator Nucleotides2.4 SOLiD; 2.4.1 Sequencing Library Preparation and Immobilization; 2.4.2 Sequencing by Ligation; 2.5 CGA Platform; 2.5.1 Sequencing Library Preparation; 2.5.2 DNA Nanoball Array; 2.5.3 Sequencing by Ligation Using Combinatorial Probe Anchors; 2.6 PacBio RS; 2.6.1 Preparation of the Sequencing Library; 2.6.2 The SMRT Cell; 2.6.3 Processive DNA Sequencing by Synthesis; 2.7 Emerging Technologies; 2.7.1 Semiconductor Sequencing; 2.7.2 Nanopore Sequencing; 2.8 Conclusions; References
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Chapter 3: Applications of High-Throughput Sequencing3.1 The Evolution of DNA Sequencing; 3.1.1 Whole Genome Shotgun Sequencing; 3.1.2 Whole Genome Re-sequencing; 3.1.3 Capture for Targeted Re-sequencing; 3.1.4 De Novo Sequencing; 3.1.5 Analysis Strategies; 3.1.5.1 Mutation Discovery; 3.1.5.2 Genomic Rearrangements; 3.2 Transcriptomics; 3.2.1 RNA-Seq; 3.2.1.1 Noncoding RNAs; 3.2.2 Analysis Strategies; 3.2.2.1 Expression Analysis; 3.3 Epigenomics; 3.3.1 DNA Methylation; 3.3.2 ChIP-Seq; 3.4 Summary; References
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Chapter 4: Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing4.1 Introduction; 4.2 Background; 4.3 Getting Started with the Next-Generation Manufacturers; 4.4 Infrastructure and Data Analysis; 4.4.1 Computational Considerations; 4.4.2 Data Dynamics; 4.4.3 Software and Post-analysis; 4.4.4 Staffing Requirements; 4.5 Applications of the Infrastructure; 4.6 Perspectives; Reference; Chapter 5: Base-Calling for Bioinformaticians; 5.1 Introduction; 5.1.1 Illumina Sequencing; 5.2 Analyzing the Illumina Sequencing Channel
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5.2.1 General Terminology of Distortion Factors
Additional Edition:
ISBN 9781461407812
Additional Edition:
Buchausg. u.d.T. Bioinformatics for high throughput sequencing New York : Springer, 2011 ISBN 9781461407812
Additional Edition:
ISBN 1461407818
Language:
English
Subjects:
Biology
DOI:
10.1007/978-1-4614-0782-9
URL:
Volltext
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