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Open Access Research article

Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes

Christian Theil Have*, Sine Zambach* and Henning Christiansen

Author Affiliations

Research group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O. Box 260, Roskilde, DK-4000, Denmark

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BMC Bioinformatics 2013, 14:118  doi:10.1186/1471-2105-14-118

Published: 4 April 2013

Abstract

Background

Pyrrolysine (the 22nd amino acid) is in certain organisms and under certain circumstances encoded by the amber stop codon, UAG. The circumstances driving pyrrolysine translation are not well understood. The involvement of a predicted mRNA structure in the region downstream UAG has been suggested, but the structure does not seem to be present in all pyrrolysine incorporating genes.

Results

We propose a strategy to predict pyrrolysine encoding genes in genomes of archaea and bacteria. We cluster open reading frames interrupted by the amber codon based on sequence similarity. We rank these clusters according to several features that may influence pyrrolysine translation. The ranking effects of different features are assessed and we propose a weighted combination of these features which best explains the currently known pyrrolysine incorporating genes. We devote special attention to the effect of structural conservation and provide further substantiation to support that structural conservation may be influential – but is not a necessary factor. Finally, from the weighted ranking, we identify a number of potentially pyrrolysine incorporating genes.

Conclusions

We propose a method for prediction of pyrrolysine incorporating genes in genomes of bacteria and archaea leading to insights about the factors driving pyrrolysine translation and identification of new gene candidates. The method predicts known conserved genes with high recall and predicts several other promising candidates for experimental verification. The method is implemented as a computational pipeline which is available on request.