title: MTide: an integrated tool for the identification of miRNA-target interaction in plants.
abstract: BACKGROUND
  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.
  
  
  METHODS
  http://bis.zju.edu.cn/MTide.
authors.affiliation: 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.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Li
authors.initials: L
authors.lastname: Jiang
authors.affiliation: 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.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Peizhen
authors.initials: P
authors.lastname: Gu
authors.affiliation: 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.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D010944:Plants / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger