Zhang Zhao, Jiang Li, Wang Jingjing, Gu Peizhen, Chen Ming
Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China and Department of Control Science and Engineering, Zhejiang University, Hangzhou 310058, China.
Bioinformatics. 2015 Jan 15;31(2):290-1. doi: 10.1093/bioinformatics/btu633. Epub 2014 Sep 24.
Small RNA sequencing and degradome sequencing (also known as parallel analysis of RNA ends) have provided rich information on the microRNA (miRNA) and its cleaved mRNA targets on a genome-wide scale in plants, but no computational tools have been developed to effectively and conveniently deconvolute the miRNA-target interaction (MTI).
A freely available package, MTide, was developed by combining modified miRDeep2 and CleaveLand4 with some other useful scripts to explore MTI in a comprehensive way. By searching for targets of a complete miRNAs, we can facilitate large-scale identification of miRNA targets, allowing us to discover regulatory interaction networks.
小RNA测序和降解组测序（也称为RNA末端平行分析）已在全基因组范围内提供了关于植物中微小RNA（miRNA）及其切割的mRNA靶标的丰富信息，但尚未开发出有效的计算工具来方便地解析miRNA-靶标相互作用（MTI）。
通过将改良的miRDeep2和CleaveLand4与其他一些有用的脚本相结合，开发了一个免费可用的程序包MTide，以全面探索MTI。通过搜索完整miRNA的靶标，我们可以促进miRNA靶标的大规模鉴定，从而发现调控相互作用网络。
