Xi Yuanxin, Li Wei
Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.
Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.
We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible.
BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.
亚硫酸氢盐测序是研究DNA胞嘧啶甲基化的一项强大技术。亚硫酸氢盐处理后进行PCR扩增可将未甲基化的胞嘧啶特异性转化为胸腺嘧啶。结合新一代测序技术，它能够检测基因组中每个胞嘧啶的甲基化状态。然而，由于搜索空间增大、亚硫酸氢盐序列复杂性降低、胞嘧啶与胸腺嘧啶的不对称比对以及多个CpG位点的异质性甲基化，将高通量亚硫酸氢盐测序读数定位到参考基因组仍然是一项巨大挑战。
我们开发了一种高效的亚硫酸氢盐测序读数定位算法BSMAP来解决上述问题。BSMAP结合了基因组哈希和按位掩码技术，以实现快速准确的亚硫酸氢盐定位。与现有的亚硫酸氢盐定位方法相比，BSMAP速度更快、更灵敏且更灵活。
BSMAP是首个通用的亚硫酸氢盐定位软件。它能够在全基因组水平上定位高通量亚硫酸氢盐测序读数，且内存和CPU使用合理。它可在http://code.google.com/p/bsmap/上根据GPL v3许可免费获取。
