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 a...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/.展开更多
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 Chinathe Fundamental Research Funds for the Central Universities(Grant No.2452020041).
文摘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/.
