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. 2018 May 1;34(9):1574-1576.
doi: 10.1093/bioinformatics/btx797.

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants

Xuan Ma  1   2 , Chunyan Liu  2 , Lianfeng Gu  3   4 , Beixin Mo  1 , Xiaofeng Cao  2 , Xuemei Chen  1   4   5
Affiliations

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants

Xuan Ma et al. Bioinformatics. .

Abstract

Summary: In plants, the targets of deeply conserved microRNAs (miRNAs) were comprehensively studied. Evidence is emerging that targets of less conserved miRNAs, endogenous target mimics (eTM) and non-canonical targets play functional roles. Existing plant miRNA prediction tools lack a cross-species conservation filter and eTM prediction function. We developed a tool named TarHunter that features a strict cross-species conservation filter and capability of predicting eTMs. TarHunter has higher recall or precision rate as compared with other tools, and the conservation filter effectively increases prediction precision. TarHunter prediction combined with degradome analysis uncovered previously neglected miRNA targets including non-canonical target sites from various plant species, which are available at the TarHunter website (http://tarhunter.genetics.ac.cn/).

Availability and implementation: The code of TarHunter is available on Github (https://github.com/XMaBio).

Contact: xuemei.chen@ucr.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
A schematic overview of TarHunter
See this image and copyright information in PMC

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