Department of Computer Science and Engineering, York University Toronto, ON M3J 1P3, Canada.
BMC Genomics. 2011;12 Suppl 2(Suppl 2):S10. doi: 10.1186/1471-2164-12-S2-S10. Epub 2011 Jul 27.
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 show that our algorithm finds a significant number of CGIs. Running an analysis on a dataset of promoters discovered 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.
Developing this new tool for the community using powerful algorithms has shown that combining analysis with CGI detection will improve the continued research within the field of epigenetics.
CpG 岛是 DNA 中的重要区域。它们通常出现在富含 GC 二核苷酸的基因的 5'端。当发生 DNA 甲基化时，会影响基因调控，有时会导致癌变。我们提出了一种使用隐马尔可夫模型和维特比算法的新检测程序。
我们的解决方案提供了许多其他 CGI 检测程序中未见的图形用户界面，并且我们将检测和分析统一在一个程序下，允许研究人员扫描遗传序列，检测显著的 CGIs，并在扫描完成后分析序列以查找任何值得注意的发现。
使用人类 21 号染色体，我们表明我们的算法发现了大量的 CGIs。对启动子数据集进行分析表明，甲基化和非甲基化 CGIs 的特征明显不同。最后，我们使用 MEME 和 MAST 在甲基化和非甲基化 CGI 启动子之间检测到明显不同的基序。
使用强大的算法为社区开发这个新工具表明，将分析与 CGI 检测相结合将提高表观遗传学领域的持续研究。
