Abstract Maize is the most important agronomic crop for human and livestock consumption, and is extensively used in modern foods, medicine and chemistry industry. In this study, coding DNA sequences(CDS) of 7402 proteins in maize were analyzed by Codon W, calculated the content of G+C at three positions of codons, ENc(effective number of codon) of genes and frequency of synonym codon usage, and determined the “optimal codons”. The results showed that the content of G+C at the third position of codons was significantly higher than that of the first and second positions, and genes prefer to the codons with C or G at the synonymous position. In addition, 27 codons were determined as the “optimal codons”, which were ending with G or C. The results provide evidences for these fields, such as molecular modification of exogenous gene to increase the expression efficiency, improving accuracy of gene prediction and genome annotation, and so on.
