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- Exploiting Codon-Triplets Association for Genome Primary Structure AnalysisPublication . Lousado, José; Oliveira, José; Moura, Gabriela; Santos, ManuelAbstract— The way evolution shapes the arrangement of synonymous codons within open reading frames (ORF) for fine tuning mRNA decoding efficiency is not yet understood. Since the ribosome has 3 tRNA binding sites, the context of triplets should be relevant to decoding fidelity and efficiency. We have developed a software application for large-scale analysis of codon-triplet associations to shed new light into this problem. The developed algorithms identify codon-triplets context biases, allowing for large scale comparative codon-triplet analysis and for identification of alterations to the standard genetic code.