ArticleBioinformatics and biology insights2013
PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation.
Article in Bioinformatics and biology insights, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
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- De Novo assembly and phylogenetic analysis of the complete mitochondrial genome of Eleutherococcus senticosus and related araliaceous species.BMC plant biology · 2025Article
- Assembly and analysis of the complete mitochondrial genome of Leonurus japonicus (Lamiaceae).Scientific reports · 2025Article
- The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution.BMC genomics · 2025Article
- Mitochondrial genome ofFrontiers in plant science · 2025Article
- Complete mitochondrial genome assembly of Juglans regia unveiled its molecular characteristics, genome evolution, and phylogenetic implications.BMC genomics · 2024Article
- Comparative Plastomics of Plantains (Plants (Basel, Switzerland) · 2024Article
- Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships.BMC plant biology · 2024Article
- Extensive characterization of 28 complete chloroplast genomes ofComputational and structural biotechnology journal · 2023Article
- Comparative analysis of mitochondrial genomes ofFrontiers in plant science · 2023Article
- Mitochondrial phylogenomics of Cuscuta (Convolvulaceae) reveals a potentially functional horizontal gene transfer from the host.Genome biology and evolution · 2022Article
- Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.Frontiers in plant science · 2022Article
- The plastid and mitochondrial genomes of Eucalyptus grandis.BMC genomics · 2019Article
- ReFernment: An R package for annotating RNA editing in plastid genomes.Applications in plant sciences · 2019Article
- Sequencing of organellar genomes of Gymnomitrion concinnatum (Jungermanniales) revealed the first exception in the structure and gene order of evolutionary stable liverworts mitogenomes.BMC plant biology · 2018Article
- Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.BMC bioinformatics · 2018Article
- The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske.International journal of molecular sciences · 2018Article
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2 authors.
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Abstract
RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 (http://www.prepact.de) with numerous enhancements of our previously developed Plant RNA Editing Prediction & Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been extended and reorganized to include 19 curated mitochondrial and 13 chloroplast genomes, now allowing to distinguish RNA editing sites from "pre-edited" sites. Queries may be run against multiple references and a new "commons" function identifies and highlights orthologous candidate editing sites congruently predicted by multiple references. Enhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simultaneously without prior user analyses.
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