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Open Access Method

A computational method to predict genetically encoded rare amino acids in proteins

Barnali N Chaudhuri and Todd O Yeates*

Author Affiliations

UCLA-DOE Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry, University of California, Los Angeles, USA

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Genome Biology 2005, 6:R79  doi:10.1186/gb-2005-6-9-r79

Published: 31 August 2005

Abstract

In several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. These rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. We report a method for such recoding prediction from genomic data, using read-through similarity evaluation. A survey across a set of microbial genomes identifies almost all the known cases as well as a number of novel candidate proteins.