CpG contents in human DNA genome are generally suppressed to only around 1% comparing with other combinations [1]. The scarcity of CpG dinucleotide can be explained by bio-chemical binding force and energy [2]. CpG islands (CGI), where high profiles of CpG sites are densely contained in some certain genome regions, play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention [3]. In vertebrate, DNA methylation usually occurs in CpG islands and adds an additional methyl to cytosine such that the gene silencing may be caused by the additional methyl. This subtle process can further give rise to different gene regulation and diverse epigenetic issues. Conventional bisulfite modification-based methods to determine the CpG island are time-consuming [4]. Although new sequencing techniques are developed for whole genome assays, it is reported to be too costly [5]. Thus, computational investigations to CpG islands is efficient and fundamental for many biological studies.
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