makeCGI is an R software package to obtain CGI from a genome. It fits two HMMs on GC content and observed to expected CpG ratio iteratively and obtain posterior probabilities for genomic regions being CpG islands. The CpG islands are then defined by thresholding the posterior probabilities.
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Wu H, Caffo B, Jaffe HA, Feinberg AP, Irizarry RA (2010)
Redefining CpG Islands Using a Hierarchical Hidden Markov Model.
Biostatistics 11(3): 499-514.