ArticleGenomics, proteomics & bioinformatics2022
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis.Functional & integrative genomics · 2025Review
- Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures.Pathogens (Basel, Switzerland) · 2024Article
- Forefronts and hotspots evolution of the nanomaterial application in anti-tumor immunotherapy: a scientometric analysis.Journal of nanobiotechnology · 2024Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- MicroRNA-mediated bioengineering for climate-resilience in crops.Bioengineered · 2021Review
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Authors and funding
8 authors.
Funding
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been 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 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. 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 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/.
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