Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA
Ting Zhang, Jingjing Zhai, Xiaorong Zhang, Lei Ling, Menghan Li, Shang Xie, Minggui Song, Chuang Ma
Genomics, Proteomics & Bioinformatics
DOI: 10.1016/j.gpb.2021.02.010
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA predictions. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users in selecting promising miRNA candidates in an interactive mode, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We illustrated the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity. The source codes and web server of iwa-miRNA are freely accessible at: http://iwa-miRNA.omicstudio.cloud/.