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

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

doi:10.1093/bioinformatics/btu633

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 journal › Article › peer-review

76 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 language	English (US)
Pages (from-to)	290-291
Number of pages	2
Journal	Bioinformatics
Volume	31
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/btu633
State	Published - Jan 15 2015
Externally published	Yes

ASJC Scopus subject areas

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

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10.1093/bioinformatics/btu633

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title = "MTide: An integrated tool for the identification of miRNA-target interaction in plants",

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.",

author = "Zhao Zhang and Li Jiang and Jingjing Wang and Peizhen Gu and Ming Chen",

year = "2015",

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doi = "10.1093/bioinformatics/btu633",

language = "English (US)",

volume = "31",

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journal = "Bioinformatics",

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T2 - An integrated tool for the identification of miRNA-target interaction in plants

AU - Zhang, Zhao

AU - Jiang, Li

AU - Wang, Jingjing

AU - Gu, Peizhen

AU - Chen, Ming

PY - 2015/1/15

Y1 - 2015/1/15

N2 - 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.

AB - 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.

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SP - 290

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JO - Bioinformatics

JF - Bioinformatics

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ER -

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

Abstract

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