Foerster Andrea M, Hetzl Jennifer, Müllner Christoph, Mittelsten Scheid Ortrun
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.
Methods Mol Biol. 2010;631:13-22. doi: 10.1007/978-1-60761-646-7_2.
Amplifying and sequencing DNA after bisulfite treatment of genomic DNA reveals the methylation state of cytosine residues at the highest resolution possible. However, a thorough analysis is required for statistical evaluation of methylation at all sites in each genomic region. Several software tools were developed to assist in quantitative evaluation of bisulfite sequencing data from complex methylation patterns occurring in plants. This chapter describes the application of Cytosine Methylation Analysis Tool for Everyone (CyMATE). From aligned sequences, CyMATE quantifies and illustrates general and pattern-specific methylation at CG, CHG, and CHH (H = A, C, or T) sites, both per sequence and per position. CyMATE is also able to perform a quality control of sequences and to detect redundancy among individual clones. The software is able to reveal methylation patterns on complementary strands by handling data from hairpin bisulfite sequencing. The tool is freely available for non-commercial use at http://www.cymate.org .
对基因组DNA进行亚硫酸氢盐处理后扩增并测序DNA，可在尽可能高的分辨率下揭示胞嘧啶残基的甲基化状态。然而，要对每个基因组区域内所有位点的甲基化进行统计评估，还需要进行全面分析。人们开发了几种软件工具，以协助对植物中出现的复杂甲基化模式的亚硫酸氢盐测序数据进行定量评估。本章介绍了面向大众的胞嘧啶甲基化分析工具（CyMATE）的应用。CyMATE根据比对序列，对每个序列和每个位置上CG、CHG和CHH（H = A、C或T）位点的总体甲基化和特定模式甲基化进行定量和说明。CyMATE还能够对序列进行质量控制，并检测单个克隆之间的冗余情况。该软件通过处理发夹亚硫酸氢盐测序数据，能够揭示互补链上的甲基化模式。该工具可在http://www.cymate.org免费用于非商业用途。
