Correlation between the usage degree of the synonymous codon and the strength of combination based on the quasi-amino acid coding

Abstract

The relative usage degree of the synonymous codon is computed and the use of preferences of the synonymous codon in 78 human genes（19967 codons） is analysed based on the quasi-amino acids coding. The results of Shi Xiufan et al. show that human genes clearly show the consistent preference in synonymous codon choice in all codon family based on the genomic genetic codes. That is, human genes prefer to use the codons with strong combination of the codon-anticodon， the codons ending with c, so that the use of the codons with moderate combination is avoided. The choice of codon in human genes is not only affected by the isochore and genome in the genome structure， but also related to the strength of combination with the codon-anticodon. All the above-mentioned factors affect the human genes，and so all the codon families clearly show the consistent preference to the synonymous codon. This study shows that the above-mentioned characteritics are more obvious when the method of quasi-amino acids coding is used.