DNA binding sites characterization by means of Rényi 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 measure 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 manuscript comparing transition frequencies (i.e. dinucelotides) and base frequencies for Shannon and parametric Renyi for a number of binding sites found in E. Coli, lambda and T7 organisms. We observe that, for the evaluated datasets, the information provided by both approaches is not redundant, as they evolve differently under increasing Renyi orders.
Perera
Alexandre
A
Centre for Biomed. Eng. Res., Tech. Univ. of Catalonia, Barcelona, Spain. Alexandre.Perera@upc.edu
Vallverdu
Montserrat
M
Claria
Francesc
F
Soria
José Manuel
JM
Caminal
Pere
P
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D019277:Entropy; D004926:Escherichia coli / Q000378:metabolism; D008957:Models, Genetic; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D009875:Operator Regions, Genetic; D011336:Probability
D009711:Nucleotides; D004247:DNA