Bioinformatics for High Throughput Sequencing

ISBN-13: 9781461407812 / Angielski / Twarda / 2011 / 255 str.

Naiara Rodriguez-Ezpeleta; Michael Hackenberg; Ana M. Aransay

Opis

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."

Spis treści

Preface.- Introduction.- Overview of Sequencing Technology Platforms.- Applications of High Throughput Sequencing.- Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing.- Base-Calling for Bioinformaticians.- De Novo Short Read Assembly.- Short Read Mapping.- DNA-Protein Interaction Analysis (ChIP-Seq).- Genome-wide Methylation Maps.- Differential Expression for RNA Sequencing (RNA-seq) Data: Mapping, Summarization, Statistical Analysis and Experimental Design.- MicroRNA Expression Profiling and Discovery.- Dissecting Splicing-Regulatory Network by Integrative Analysis of HITS-CLIP data.- Analysis of Metagenomics Data.- High Throughput Sequencing Data Analysis Software: Current State and Future Developments.- Index.

Blurb

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.