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CGI-HMM package uses Hidden-Markov Model(HMM) based algorithm to find CpG island(CGI) for whole genome/chromosome sequences, or any other nucleotide sequences in fasta format. It reports length of CGI, start & end position, GC%, OEratio, and average CpG distance in detected CGI regions. It also comes with a GetProb module to calculate initial and transition probability for HMM use.

Note: This is a personal effort without any funding support.

Source code type: c++

System requirement
Passed test (whole genome) on 32bit ubuntu with 2G memory. Recommend 64bit system with >=2G memory

2013-1-29 Added MAC version

Report bug to ruansun@163.com