Li Min, Huang Ping, Yan Xiaodong, Wang Jianxin, Pan Yi, Wu Fang-Xiang
School of Information Science and Engineering, Central South University, Changsha, 410083, China.
Department of Computer Science, Georgia State University, Atlanta, GA, 30302-4110, USA.
BMC Bioinformatics. 2017 Oct 16;18(Suppl 12):410. doi: 10.1186/s12859-017-1827-1.
Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfite treatment, traditional mapping tools do not work well with such methylation experimental reads. Traditional aligners are not designed for mapping bisulfite-treated reads, where the un-methylated 'C's are converted to 'T's.
In this paper, we develop a reliable and visual tool, named VAliBS, for mapping bisulfate sequences to a genome reference. VAliBS works well even on large scale data or high noise data. By comparing with other state-of-the-art tools (BisMark, BSMAP, BS-Seeker2), VAliBS can improve the accuracy of bisulfite mapping. Moreover, VAliBS is a visual tool which makes its operations more easily and the alignment results are shown with colored marks which makes it easier to be read. VAliBS provides fast and accurate mapping of bisulfite-converted reads, and a friendly window system to visualize the detail of mapping of each read.
VAliBS works well on both simulated data and real data. It can be useful in DNA methylation research. VALiBS implements an X-Window user interface where the methylation positions are visual and the operations are friendly.
甲基化是DNA的一种常见修饰。在医学领域，研究甲基化与疾病之间的关联一直是一个非常重要且热门的话题。由于亚硫酸氢盐处理的特殊过程，传统的映射工具在处理此类甲基化实验读数时效果不佳。传统的比对器并非为映射经亚硫酸氢盐处理的读数而设计，在这种读数中，未甲基化的“C”会被转化为“T”。
在本文中，我们开发了一种可靠且可视化的工具，名为VAliBS，用于将亚硫酸氢盐序列映射到基因组参考序列上。即使在大规模数据或高噪声数据上，VAliBS也能很好地工作。通过与其他最先进的工具（BisMark、BSMAP、BS-Seeker2）进行比较，VAliBS可以提高亚硫酸氢盐映射的准确性。此外，VAliBS是一种可视化工具，这使得其操作更加简便，并且比对结果以彩色标记显示，更易于阅读。VAliBS提供了快速且准确的亚硫酸氢盐转化读数映射，以及一个友好的窗口系统来可视化每个读数的映射细节。
VAliBS在模拟数据和真实数据上均表现良好。它在DNA甲基化研究中可能会很有用。VALiBS实现了一个X窗口用户界面，其中甲基化位置可视化且操作友好。
