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Methods Mol Biol. 2010;628:275-96. doi: 10.1007/978-1-60327-367-1_15.

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Author information

1
Max-Planck-Institut für Informatik, Saarbrücken, Germany.

Abstract

Modern life sciences are becoming increasingly data intensive, posing a significant challenge for most researchers and shifting the bottleneck of scientific discovery from data generation to data analysis. As a result, progress in genome research is increasingly impeded by bioinformatic hurdles. A new generation of powerful and easy-to-use genome analysis tools has been developed to address this issue, enabling biologists to perform complex bioinformatic analyses online - without having to learn a programming language or downloading and manually processing large datasets. In this tutorial paper, we describe the use of EpiGRAPH (http://epigraph.mpi-inf.mpg.de/) and Galaxy (http://galaxyproject.org/) for genome and epigenome analysis, and we illustrate how these two web services work together to identify epigenetic modifications that are characteristics of highly polymorphic (SNP-rich) promoters. This paper is supplemented with video tutorials (http://tinyurl.com/yc5xkqq), which provide a step-by-step guide through each example analysis.

PMID:
20238087
DOI:
10.1007/978-1-60327-367-1_15
[Indexed for MEDLINE]

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