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

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 t

SUBMITTER: Theil Have C 

PROVIDER: S-EPMC3639795 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature