Classification of Genes Based on Synonymous Codon Usage

Introduction The prediction of the function of a novel gene remains to be a challenging problem. Given a piece of coding sequence, one can deduce its function by finding homologous genes using sequence or protein structural alignment. One can also perform gene expression measurements or gene knockout experiments to determine the function of a gene. However, a gene may not have homology with any known gene and experiments can be expensive. It would therefore be beneficial if the function of a gene can be predicted from the characteristics of its coding sequence. One such characteristics is synonymous codon usage.