Correlating CpG islands, motifs, and sequence variants in human chromosome 21

CpG islands are important regions in DNA. They usually appear at the 5´ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcinogenesis. We propose a new detection program using a hidden Markov model alongside the Viterbi algorithm. Our solution provides a graphical user interface not seen in many of the other CGI detection programs and we unify the detection and analysis under one program to allow researchers to scan a genetic sequence, detect the significant CGIs, and analyze the sequence once the scan is complete for any noteworthy findings. Using human chromosome 21, we run an analysis on a dataset of promoters and discover that the characteristics of methylated and unmethylated CGIs are significantly different. Finally, we detected significantly different motifs between methylated and unmethylated CGI promoters using MEME and MAST.