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

Zhao Zhang, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen

Research output: Contribution to journalArticlepeer-review

54 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)290-291
Number of pages2
JournalBioinformatics
Volume31
Issue number2
DOIs
StatePublished - Jan 15 2015
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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