MTide – an integrated tool for the identification of miRNA-target interaction in plants

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.

rna-seq

Availability and implementation: http://bis.zju.edu.cn/MTide

Contact: mchen@zju.edu.cn

Zhang Z, Jiang L, Wang J, Gu P, Chen M. (2014) MTide: an integrated tool for the identification of miRNA-target interaction in plants. Bioinformatics [Epub ahead of print]. [abstract]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.