MethylViewer

About this program

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 program will accept sequence data from plain text files as well as a variety of electropherogram formats. Using electropherogram trace files allows the alignment to be edited with reference to the trace data.

Once the program as created the alignment it can be saved as a text file or an image file. These images can show the data as a classical square grid or a series of 'lollipops' equally spaced or spaced relative to their position in the CpG island.

This program and its instruction file is currently hosted on mirror of my old department web site and can obtained from here. A copy of the user guide on this site can be found here.

Citation

Pardo C, Carr IM (joint first name author), Hoffman C, Darst R, Markham AF, Bonthron DT, Kladde M. (2011). MethylViewer: computational analysis and editing for bisulphite sequencing and Methyltransferase Accessibility Protocol for Individual Templates (MAPit) projects. Nucleic Acids Res. 1;39(1):e5

Computer requirements

This program runs on Microsoft Windows, using the .NET 2.0 environment which can be obtained from here.