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

作     者：Ting Zhang Jingjing Zhai Xiaorong Zhang Lei Ling Menghan Li Shang Xie Minggui Song Chuang Ma Ting Zhang;Jingjing Zhai;Xiaorong Zhang;Lei Ling;Menghan Li;Shang Xie;Minggui Song;Chuang Ma

作者机构：State Key Laboratory of Crop Stress Biology for Arid AreasCenter of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling 712100China Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest RegionMinistry of Agriculture and Rural AffairsNorthwest A&F UniversityYangling 712100China College of Plant ScienceTibet Agricultural and Animal Husbandry UniversityLinzhi 860006China College of Information EngineeringNorthwest A&F UniversityYangling 712100China 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2022年第20卷第3期

页      面：557-567页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 07[理学] 08[工学] 

基　　金：supported by the National Natural Science Foundation of China(Grant No.31570371) the Youth 1000-Talent Program of China,the Hundred Talents Program of Shaanxi Province of China the Fundamental Research Funds for the Central Universities(Grant No.2452020041) 

主　　题：Galaxy Interactive annotation Manual inspection MicroRNA Platform 

摘      要：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://***/.