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About this program

This program is designed to speed up the characterisation of mammalian CpG islands by aligning DNA sequences from bisulphite-modified DNA to the genomic sequence of the CpG island. While been a simple task it is a tedious and error prone task when done manually.

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, PowerPoint presentation or 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.

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

The program has been published in NAR and is recommended by ABI as part of its DNA methylation protocol.


Carr IM, Valleley EMA, Cordery SF, Markham AF & Bonthron DT (2007). Sequence analysis and editing for bisulphite genomic sequencing projects. Nucleic Acids Res., 35:e79

Computer requirements

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

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