Skip Navigation


Bioinformatics Advance Access originally published online on July 1, 2004
Bioinformatics 2004 20(17):3214-3220; doi:10.1093/bioinformatics/bth387
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/17/3214    most recent
bth387v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (7)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bundschuh, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bundschuh, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Computational prediction of RNA editing sites

R. Bundschuh

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

Received on May 8, 2003; accepted on June 25, 2004
Advance Access Publication July 1, 2004

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.

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
C. Beargie, T. Liu, M. Corriveau, H. Y. Lee, J. Gott, and R. Bundschuh
Genome annotation in the presence of insertional RNA editing
Bioinformatics, November 15, 2008; 24(22): 2571 - 2578.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. M. Gott, N. Parimi, and R. Bundschuh
Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs
Nucleic Acids Res., September 7, 2005; 33(16): 5063 - 5072.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.