CpG Islands
Find targets for DNA methylation by predicting CpG islands
Requires Geneious 3.6+
DNA methylation is an important part of gene regulation as it can prevent proteins binding to a gene in transcription. Using the Hidden Markov models described by Richard Durbin, the CpG Plugin will generate a nucleotide sequence graph which will predict how likely a region of your sequence is a possible methylation site.
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, select a nucleotide sequence and the CpG island graph will appear. Options are available on the Graphs tab of the controls to the right of the Sequence view.