ArticleBioinformatics (Oxford, England)2008
Genome annotation in the presence of insertional RNA editing.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Comparison of insertional RNA editing in Myxomycetes.PLoS computational biology · 2012Article
- Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA.Nucleic acids research · 2011Article
- RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis.Current genetics · 2010Article
- RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum.RNA (New York, N.Y.) · 2010Article
- Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria.RNA (New York, N.Y.) · 2010Article
- Distinct roles for sequences upstream of and downstream from Physarum editing sites.RNA (New York, N.Y.) · 2009Article
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Authors and funding
6 authors.
Funding
Abstract
motivationInsertional RNA editing renders gene prediction very difficult compared to organisms without such RNA editing. A case in point is the mitochondrial genome of Physarum polycephalum in which only about one-third of the number of genes that are to be expected given its length are annotated. Thus, gene prediction methods that explicitly take into account insertional editing are needed for successful annotation of such genomes.
resultsWe annotate the mitochondrial genome of P.polycephalum using several different approaches for gene prediction in organisms with insertional RNA editing. We computationally validate our annotations by comparing the results from different methods against each other and as proof of concept experimentally validate two of the newly predicted genes. We more than double the number of annotated putative genes in this organism and find several intriguing candidate genes that are not expected in a mitochondrial genome. AVAILABILITY: The C source code of the programs described here are available upon request from the corresponding author.
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Registered trials
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