CgiHunter

A software tool for exhaustive CpG island annotation

CpG islands are genome regions with an elevated Guanine + Cytosine content (GC content) and a higher CpG dinucleotide frequency than observed in the bulk genome. More than half of the human gene promoters colocalize with CpG islands and their methylation status has been shown to correlate with the expression level of the associated genes. As a consequence, CpG islands are assumed to be hotspots of epigenetic regulation.

However, an exact definition of CpG islands is still not agreed upon. The CgiHunter software tool follows the original sequence based CpG island definition proposed by Gardiner-Garden and Frommer. They defined three requirements a genome region has to fulfill to qualify as CpG island: a minimal length, a minimal GC content and a minmal ratio of its observed over its expected CpG dinucleotide frequency. Unlike many other search heuristics, the CgiHunter algorithm has been proven to identify all genome regions that meet this criteria and results in robust and consistent CpG island annotations.

Currently, the paper that describs the method in detail, is under revision. If you have questions regarding the underlying algorithm, please contact us.

There are two options for the usage of CgiHunter. You can either download the software from our website, or in the case of small queries, use our online webservice.

If you have further questions, do not hesitate to contact us (CgiHunter@mpi-inf.mpg.de) or visit our FAQ page.