CpG-Profile

Due to the spontaneous deamination of 5'-methylcytosine into thymine, the number of CpG sites is less than expected in vertebrate genomes. However, there are a large number of CpG dinucleotides clustered in some loci, known as CpG islands (CGIs), where CpG dinucleotides are free from methylation.

Method：CpG-Profile is a novel extension of GC-Profile. The basic idea of the CpG-Profile algorithm is to modify the genome order index S(P) in GC-Profile to find CpG islands (see following equation). The web server is developed with python and adopts the classical LAMP framework (Linux + Apache + MariaDB + PHP). For the complex recursive segmentation, the calculation is accelerated by using Cython.