ArticleApplications in plant sciences2019
ReFernment: An R package for annotating RNA editing in plastid genomes.
Article in Applications in plant sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Comparative plastome analysis of the Vandenboschia radicans complex in Korea: insights into its evolutionary history.BMC plant biology · 2026Article
- Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages.The New phytologist · 2026Article
- Sequencing of the complete plastome of the thermal adder's-tongue fern,Mitochondrial DNA. Part B, Resources · 2024Article
- Progress, challenge and prospect of plant plastome annotation.Frontiers in plant science · 2023Review
- Article
- Variation in plastid genomes in the gynodioecious species Silene vulgaris.BMC plant biology · 2019Article
- ReFernment: An R package for annotating RNA editing in plastid genomes.Applications in plant sciences · 2019Article
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Authors and funding
2 authors.
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Abstract
premise of the studyIn the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts. METHODS AND
resultsWe developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.
conclusionsCompared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of plastome sequences for taxa with high levels of RNA editing.
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