DNA binding site characterization by means of Renyi entropy measures on nucleotide transitions

In this work, parametric information-theory measures for the characterization of binding sites in DNA are extended with the use of transitional probabilities on the sequence. We propose the use of parametric uncertainty measures such as Renyi entropies obtained from the transition probabilities for the study of the binding sites, in addition to nucleotide frequency-based Renyi measures. Results are reported in this work comparing transition frequencies (i.e., dinucleotides) and base frequencies for Shannon and parametric Renyi entropies for a number of binding sites found in E. Coli, lambda, and T7 organisms. We observe that the information provided by both approaches is not redundant. Furthermore, under the presence of noise in the binding site matrix we observe overall improved robustness of nucleotide transition-based algorithms when compared with nucleotide frequency-based method.