Computational analysis of stop codon readthrough in D.melanogaster.
BACKGROUND
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.


BACKGROUND
Source code of the system is available upon request.
Sato
Misaki
M
Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
Umeki
Hitomi
H
Saito
Rintaro
R
Kanai
Akio
A
Tomita
Masaru
M
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D018388:Codon, Terminator / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D018388:Codon, Terminator; D029721:Drosophila Proteins