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Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

Genomics, Proteomics & Bioinformatics 2022年第3期20卷 557-567页

作者： Ting Zhang Jingjing Zhai Xiaorong Zhang Lei Ling Menghan Li Shang Xie Minggui Song Chuang Ma State Key Laboratory of Crop Stress Biology for Arid Areas Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling 712100China Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region Ministry of Agriculture and Rural AffairsNorthwest A&F UniversityYangling 712100China College of Plant Science Tibet Agricultural and Animal Husbandry UniversityLinzhi 860006China College of Information Engineering Northwest A&F UniversityYangling 712100China

MicroRNAs(miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been accelerated with the development of highthroughput 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 prediction tools. 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. iwamiRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With fexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We also illustrate 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/.

关键词： Galaxy Interactive annotation manual inspection MicroRNA Platform

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