Cluster analysis of the codon use frequency of MHC genes and genes coding for proteins with different fingerprints

Summary form only received as follows: The relative synonymous codon use frequencies (RSCU) of 135 MHC genes from four mammal species are analyzed using hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias. RSCU values of 71 genes coding for proteins with two different fingerprints are also studied and these 71 genes can be clearly differentiated into two groups according to the difference in codon usage bias. This indicates that codon usage is closely related to protein high-level structure. The conclusion may be useful in gene classification and prediction of gene function and protein spatial structure.