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Bioinformatics Advance Access published online on September 25, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn487
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Genome annotation in the presence of insertional RNA editing

Christina Beargie a, Tsunglin Liu b, Mark Corriveau c, Ha Youn Lee d, Jonatha Gott c and Ralf Bundschuh e,*

aCOSI, 333 West Broad Street, Columbus, OH 43215, bResearch Center for Biodiversity, Academia Sinica, Taipei, Taiwan, cCenter for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, dDepartment of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 630 Rochester, NY 14642, eDepartments of Physics and Biochemistry and the RNA Consortium, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117

*To whom correspondence should be addressed. Dr. Ralf Bundschuh, E-mail: bundschuh{at}mps.ohio-state.edu


  Abstract

Motivation: 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 Physarum 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.

Contact: bundschuh{at}mps.ohio-state.edu

Associate Editor: Ivo Hofacker

Received on April 9, 2008; revised on August 25, 2008; accepted on September 11, 2008

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