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Bioinformatics Advance Access published online on July 1, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth387
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 8, 2003
Revised June 25, 2004
Accepted June 25, 2004

Article

Computational prediction of RNA editing sites

R. Bundschuh 1*

1 Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, OH 43210-1106, USA

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


  Abstract

Motivation: Some organisms edit their messenger RNA resulting in differences between the genomic sequence for a gene and the corresponding messenger RNA sequence. This difference complicates experimental and computational attempts to find and study genes in organisms with RNA editing even if the full genomic sequence is known. Nevertheless, knowledge of these editing sites is crucial for understanding the editing machinery of these organisms.

Results: We present a computational technique that predicts the position of editing sites in the genomic sequence. It uses a statistical approach drawing on the protein sequences of related genes and general features of editing sites of the organism. We apply the method to the mitochondrion of the slime mold Physarum polycephalum. It correctly predicts over 90% of the amino acids and over 70% of the editing sites.

Availability: The source code is available upon request from the author.


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This article has been cited by other articles:


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C. Beargie, T. Liu, M. Corriveau, H. Y. Lee, J. Gott, and R. Bundschuh
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