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In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. <jats:italic>Candida albicans<\/jats:italic> exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-8-444","type":"journal-article","created":{"date-parts":[[2007,11,29]],"date-time":"2007-11-29T19:14:09Z","timestamp":1196363649000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Codon-triplet context unveils unique features of the Candida albicans protein coding genome"],"prefix":"10.1186","volume":"8","author":[{"given":"Gabriela R","family":"Moura","sequence":"first","affiliation":[]},{"given":"Jos\u00e9 P","family":"Lousado","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Pinheiro","sequence":"additional","affiliation":[]},{"given":"Laura","family":"Carreto","sequence":"additional","affiliation":[]},{"given":"Raquel M","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 L","family":"Oliveira","sequence":"additional","affiliation":[]},{"given":"Manuel AS","family":"Santos","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,11,29]]},"reference":[{"key":"1157_CR1","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1006\/jmbi.1996.0428","volume":"260","author":"H Dong","year":"1996","unstructured":"Dong H, Nilsson L, Kurland CG: Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. 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