ArticleBMC bioinformatics2019
FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed, 1 citations in OpenAlex.
- The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.BMC bioinformatics · 2019Article
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6 authors at 3 institutions in 2 countries.
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Abstract
backgroundRNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon.
resultsWe present FEDRO, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c→u) editing substitutions which occur in the mitochondrial genome (mtDNA) of a given input plant. The goal is to predict putative proteins of plants mitochondria that have not been yet annotated. In order to validate the generated ORFs, a screening is performed by checking for sequence similarity or presence in active transcripts of the same or similar organisms. We illustrate the functionalities of our framework on a model organism.
conclusionsThe proposed tool may be used also on other organisms and genomes. FEDRO is publicly available at http://math.unipa.it/rombo/FEDRO .
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