Abstract: The usages of k-mer (mainly k=6) were analyzed based on Markov chain model,k-mer occurrence frequencies and weighted Markov chain model respectively,and a fuzzy relative entropy was defined to measure the difference between the structures of two DNA sequences.The lowly-transcribed gene promoters were taken as a control set,the fuzzy relative entropies of other promoters of the genes with higher transcriptional frequencies were calculated.It was found that there was a linear positive correlation between the fuzzy relative entropies and transcription frequencies.In general,the more different between the transcriptional frequencies of two genes,the more different between their sequences structures of the promoters.This result suggested that there existed a certain correlation between the sequences structures of promoters and the transcriptional frequencies in yeast genes.Compared with the fuzzy relative entropy under Markov chain model or k-mer occurrence frequency,the fuzzy relative entropy under weighted Markov chain model could measure the difference of gene promoter sequence structures more effectively.This showed that the weighted Markov chain model,especially 4-order model,could better characterize the sequence organizations of yeast gene promoters.