title: DNA binding sites characterization by means of Rényi entropy measures on nucleotide transitions.
abstract: 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.
authors.affiliation: Centre for Biomed. Eng. Res., Tech. Univ. of Catalonia, Barcelona, Spain. Alexandre.Perera@upc.edu
authors.forename: Alexandre
authors.initials: A
authors.lastname: Perera
authors.forename: Montserrat
authors.initials: M
authors.lastname: Vallverdu
authors.forename: Francesc
authors.initials: F
authors.lastname: Claria
authors.forename: José Manuel
authors.initials: JM
authors.lastname: Soria
authors.forename: Pere
authors.initials: P
authors.lastname: Caminal
mesh_terms: 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
chemical_list: D009711:Nucleotides; D004247:DNA