UnMeRFi (Under-Methylated Region Finder) estimates under-methylated regions in an unspecified DNA sequence. The program works by using a moving window (the size of which can be specified by the user) and by assessing the likelihood of that window to be under-methylated. As a final step windows passing the threshold are joined to form contiguous under-methylated regions.
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Straussman et al
Developmental programming of CpG island methylation profiles in the human genome
Nature Structural & Molecular Biology 16, 564 – 571 (2009)