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

Bioinformatics. 2015 Jan 15;31(2):290-1. doi: 10.1093/bioinformatics/btu633. Epub 2014 Sep 24.


Motivation: 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).

Results: 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.

Availability and implementation:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Plants / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Sequence Analysis, RNA / methods*
  • Software*


  • MicroRNAs
  • RNA, Messenger