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Nucleic Acids Research, 2000, Vol. 28, No. 5 1053-1058
© 2000 Oxford University Press

MethTools—a toolbox to visualize and analyze DNA methylation data

Christoph Grunau, Ruben Schattevoy, Niels Mache1 and André Rosenthal*

Department of Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstrasse 11, D-07745 Jena, Germany and 1Institute of Parallel and Distributed High Performance Systems, IPVR, Breitwiesenstrasse 20–22, D-70565 Stuttgart, Germany

The Bisulfite Genomic Sequencing technique has found wide acceptance for the generation of DNA-methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil (and subsequent conversion to thymine via PCR), whereas 5-methylcytosine residues remain unchanged. Methylation maps are created by the comparison of bisulfite converted sequences with the untreated genomic sequence. ‘MethTools’ is a collection of software tools that replaces the time-consuming manual comparison process, generates graphical outputs of methylation patterns and methyl­ation density, estimates the systematic error of the experiment and searches for conserved methylated nucleotide patterns. The programs are written in Perl 5 and C, and the source code can be downloaded. All tools run independently but the programs are interfaced. Thus, a script can perform the entire analysis procedure automatically. In addition, a web-based remote analysis service is offered. Both the source code and the remote analysis are available at http://genome.imb-jena.de/methtools/

* To whom correspondence should be addressed. Tel: +49 3641 65 62 40; Fax: +49 3641 65 62 55; Email: arosenth@imb-jena.de Present address: Ruben Schattevoy, Max-Planck-Institut of Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried/Munich, Germany


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