Bioinformatics for High Throughput Sequencing

✍ Scribed by Naiara Rodríguez-Ezpeleta, Ana M. Aransay (auth.), Naiara Rodríguez-Ezpeleta, Michael Hackenberg, Ana M. Aransay (eds.)

Publisher: Springer-Verlag New York
Year: 2012
Tongue: English
Leaves: 266
Edition: 1
Category: Library

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✦ Synopsis

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.

✦ Table of Contents

Front Matter....Pages i-xi
Introduction....Pages 1-9
Overview of Sequencing Technology Platforms....Pages 11-25
Applications of High-Throughput Sequencing....Pages 27-53
Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing....Pages 55-65
Base-Calling for Bioinformaticians....Pages 67-83
De Novo Short-Read Assembly....Pages 85-105
Short-Read Mapping....Pages 107-125
DNA–Protein Interaction Analysis (ChIP-Seq)....Pages 127-149
Generation and Analysis of Genome-Wide DNA Methylation Maps....Pages 151-167
Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design....Pages 169-190
MicroRNA Expression Profiling and Discovery....Pages 191-208
Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data....Pages 209-218
Analysis of Metagenomics Data....Pages 219-229
High-Throughput Sequencing Data Analysis Software: Current State and Future Developments....Pages 231-248
Back Matter....Pages 249-255

✦ Subjects

Bioinformatics; Human Genetics; Biomedicine general

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