Genome annotation in the presence of insertional RNA editing

Christina Beargie, Tsung-lin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, Ralf Bundschuh

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)2571-2578
Number of pages8
JournalBioinformatics
Volume24
Issue number22
DOIs
Publication statusPublished - 2008 Nov 1

Fingerprint

RNA Editing
RNA
Annotation
Genome
Genes
Gene
Mitochondrial Genome
Prediction
Physarum polycephalum

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Beargie, C., Liu, T., Corriveau, M., Lee, H. Y., Gott, J., & Bundschuh, R. (2008). Genome annotation in the presence of insertional RNA editing. Bioinformatics, 24(22), 2571-2578. https://doi.org/10.1093/bioinformatics/btn487
Beargie, Christina ; Liu, Tsung-lin ; Corriveau, Mark ; Lee, Ha Youn ; Gott, Jonatha ; Bundschuh, Ralf. / Genome annotation in the presence of insertional RNA editing. In: Bioinformatics. 2008 ; Vol. 24, No. 22. pp. 2571-2578.
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Beargie, C, Liu, T, Corriveau, M, Lee, HY, Gott, J & Bundschuh, R 2008, 'Genome annotation in the presence of insertional RNA editing', Bioinformatics, vol. 24, no. 22, pp. 2571-2578. https://doi.org/10.1093/bioinformatics/btn487

Genome annotation in the presence of insertional RNA editing. / Beargie, Christina; Liu, Tsung-lin; Corriveau, Mark; Lee, Ha Youn; Gott, Jonatha; Bundschuh, Ralf.

In: Bioinformatics, Vol. 24, No. 22, 01.11.2008, p. 2571-2578.

Research output: Contribution to journalArticle

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Beargie C, Liu T, Corriveau M, Lee HY, Gott J, Bundschuh R. Genome annotation in the presence of insertional RNA editing. Bioinformatics. 2008 Nov 1;24(22):2571-2578. https://doi.org/10.1093/bioinformatics/btn487