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Updated: Nov 23, 2025
mirMachine: A One-Stop Shop for Plant miRNA Annotation
Published on: May 1, 2021
MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants
Guillem Ylla1,2, Tianyuan Liu1, Ana Conesa1
1Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
Motivation:
microRNAs (miRNAs) are essential components of gene expression regulation at the post-transcriptional level. miRNAs have a well-defined molecular structure and this has facilitated the development of computational and high-throughput approaches to predict miRNAs genes. However, due to their short size, miRNAs have often been incorrectly annotated in both plants and animals. Consequently, published miRNA annotations and miRNA databases are enriched for false miRNAs, jeopardizing their utility as molecular information resources. To address this problem, we developed MirCure, a new software for quality control, filtering and curation of miRNA candidates. MirCure is an easy-to-use tool with a graphical interface that allows both scoring of miRNA reliability and browsing of supporting evidence by manual curators.
Results:
Given a list of miRNA candidates, MirCure evaluates a number of miRNA-specific features based on gene expression, biogenesis and conservation data, and generates a score that can be used to discard poorly supported miRNA annotations. MirCure can also curate and adjust the annotation of the 5p and 3p arms based on user-provided small RNA-seq data. We evaluated MirCure on a set of manually curated animal and plant miRNAs and demonstrated great accuracy. Moreover, we show that MirCure can be used to revisit previous bona fide miRNAs annotations to improve miRNA databases.
Availability And Implementation:
The MirCure software and all the additional scripts used in this project are publicly available at https://github.com/ConesaLab/MirCure. A Docker image of MirCure is available at https://hub.docker.com/r/conesalab/mircure.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Insights
MirCure software enhances microRNA (miRNA) annotation accuracy by filtering false candidates and improving database reliability. This tool ensures higher quality miRNA data for researchers studying gene expression regulation.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- microRNAs (miRNAs) regulate gene expression post-transcriptionally.
- Short miRNA sequences lead to frequent misannotations in plants and animals.
- Existing miRNA databases contain numerous false miRNA entries, limiting their utility.
Purpose of the Study:
- To develop MirCure, a novel software for quality control, filtering, and curation of miRNA candidates.
- To improve the accuracy and reliability of miRNA annotations and databases.
Main Methods:
- MirCure evaluates miRNA candidates using gene expression, biogenesis, and conservation data.
- The software provides a reliability score to identify poorly supported annotations.
- MirCure can adjust 5p and 3p arm annotations using small RNA-seq data.
Main Results:
- MirCure demonstrated high accuracy in evaluating manually curated animal and plant miRNAs.
- The software effectively filters false miRNA annotations.
- Revisiting existing miRNA annotations with MirCure improved database quality.
Conclusions:
- MirCure is a valuable tool for ensuring the quality of miRNA annotations.
- The software aids in the curation of reliable miRNA databases.
- MirCure contributes to more accurate molecular information resources for gene expression studies.
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