MethylViewer
Interactive data analysis of bisulphite DNA sequencing to map chromatin structure using DNA methyltransferases
Sequencing of bisulphite-modified DNA is a widely-used method for analysis of genomic methylation. If a non-native DNA methylase is used to modify chromatin-bound DNA, the methylation pattern can be used to identify the binding sites of DNA-binding proteins.
MethylViewer was developed from CpGviewer and aims to be a simple integrated tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases.
The primary MethylViewer editing window looks like this:
MethylViewer will also show the positions of unconverted cytosine residues:
MethylViewer offers a facility for designing primers for bisulphite-treated templates, and can export complex figures for publication, like this one:
(Click to display the image at full size.)
Feature guide
A “walk-through” explanation, with screenshots, of MethylViewer usage:
Download
The download page currently offers a preview version of the MethylViewer program and some sample data files, used in the examples shown in the online Guide and in the manuscript.
The MethylViewer program has been written by Ian Carr. It is still undergoing testing, and any feedback on its features or performance would be very welcome.
Citation
Pardo C, Carr IM, Hoffman C, Darst R, Markham AF, Bonthron DT, Kladde M
MethylViewer: computational analysis and editing for bisulphite sequencing and Methyltransferase Accessibility Protocol for Individual Templates (MAPit) projects.
Nucleic Acids Res. 2011 Jan 1;39(1):e5