Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (11)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Sato, M.
Right arrow Articles by Tomita, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sato, M.
Right arrow Articles by Tomita, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 11 2003
Pages 1371-1380
© 2003 Oxford University Press

Computational analysis of stop codon readthrough in D.melanogaster

Misaki Sato 1,2, Hitomi Umeki 1,3, Rintaro Saito 1,*, Akio Kanai 1 and Masaru Tomita 1,3

1 Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
2 Faculty of Policy Management, Keio University, Fujisawa, 252-8520, Japan
3 Faculty of Environmental Information, Keio University, Fujisawa, 252-8520, Japan

Received on October 24, 2002 ; revised on January 1, 2003 ; accepted on February 25, 2003

Motivation: Readthrough is an unusual process in which a stop codon is misread or skipped. Recently it has been shown that some translation is regulated by the readthrough reactions although the complete mechanism is not clear. Therefore, the discovery of ‘readthrough genes’ is important for further investigation of their cellular roles, which may provide additional insights into the mechanism of translational regulation.

Results: We constructed a system that lists candidates of readthrough genes based on the existence of a ‘protein motif’ at the 3' untranslated region (UTR). Using this system, we extracted 85 candidates from 4082 nucleic acid sequences of Drosophila melanogaster in GenBank database. The sequences of these candidates had a slightly more stable secondary structure and different base preferences compared to the non-candidates. As these features are known to have an effect on readthrough events, we would like to suggest that these candidates contain actual readthrough genes.

Availability: Source code of the system is available upon request.

Contact: rsaito{at}sfc.keio.ac.jp

* To whom correspondence should be addressed.


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
 GeneticsHome page
S. Berger, N. A. Bulgakova, F. Grawe, K. Johnson, and E. Knust
Unraveling the Genetic Complexity of Drosophila stardust During Photoreceptor Morphogenesis and Prevention of Light-Induced Degeneration
Genetics, August 1, 2007; 176(4): 2189 - 2200.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
J. REHWINKEL, I. LETUNIC, J. RAES, P. BORK, and E. IZAURRALDE
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
RNA, October 1, 2005; 11(10): 1530 - 1544.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Bekaert, H. Richard, B. Prum, and J.-P. Rousset
Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
Genome Res., October 1, 2005; 15(10): 1411 - 1420.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. R. MacPherson, V. P. Pollock, L. Kean, T. D. Southall, M. E. Giannakou, K. E. Broderick, J. A. T. Dow, R. C. Hardie, and S. A. Davies
Transient Receptor Potential-Like Channels Are Essential for Calcium Signaling and Fluid Transport in a Drosophila Epithelium
Genetics, March 1, 2005; 169(3): 1541 - 1552.
[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.