title: Genome annotation in the presence of insertional RNA editing.
abstract: BACKGROUND
  Insertional 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.
  
  
  RESULTS
  We 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.
  
  
  BACKGROUND
  The C source code of the programs described here are available upon request from the corresponding author.
authors.affiliation: COSI, 333 West Broad Street, Columbus, OH 43215, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Beargie
authors.forename: Tsunglin
authors.initials: T
authors.lastname: Liu
authors.forename: Mark
authors.initials: M
authors.lastname: Corriveau
authors.forename: Ha Youn
authors.initials: HY
authors.lastname: Lee
authors.forename: Jonatha
authors.initials: J
authors.lastname: Gott
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
mesh_terms: D000818:Animals; D054629:Genome, Mitochondrial / Q000235:genetics; D018503:Genome, Protozoan / Q000235:genetics*; D016839:Physarum polycephalum / Q000235:genetics*; D017393:RNA Editing / Q000235:genetics*