ArticleBioinformatics (Oxford, England)2017
miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- A first comparison of miRNA profiles of Antarctic Deschampsia antarctica ecotypes with Triticum aestivum upon single or combined salt and drought stresses.Functional & integrative genomics · 2026Article
- Article
- Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis.Functional & integrative genomics · 2025Review
- An intron-split microRNA mediates cleavage of the mRNA encoded by low phosphate root in Solanaceae.Planta · 2025Article
- Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.Genomics, proteomics & bioinformatics · 2022Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise.Nucleic acids research · 2021Article
- Establishment of Repertoire of Placentome-Associated MicroRNAs and Their Appearance in Blood Plasma Could Identify Early Establishment of Pregnancy in Buffalo (Frontiers in cell and developmental biology · 2021Article
- microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation.BMC genomics · 2020Article
- PAREameters: a tool for computational inference of plant miRNA-mRNA targeting rules using small RNA and degradome sequencing data.Nucleic acids research · 2020Article
- PmiREN: a comprehensive encyclopedia of plant miRNAs.Nucleic acids research · 2020Article
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- miPIE: NGS-based Prediction of miRNA Using Integrated Evidence.Scientific reports · 2019Article
- miRNomes involved in imparting thermotolerance to crop plants.3 Biotech · 2018Review
- The evolutionary dynamics of microRNAs in domestic mammals.Scientific reports · 2018Article
- The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.Bioinformatics (Oxford, England) · 2018Article
- PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules.Nucleic acids research · 2018Article
- New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants.RSC advances · 2018Article
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9 authors.
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Abstract
motivationMicroRNAs are a class of ∼21-22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure.
resultsWe test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. AVAILABILITY AND IMPLEMENTATION: miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. CONTACT: v.moulton@uea.ac.uk or s.moxon@uea.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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