title: Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices.
abstract: The importance of the promoter sequences in the function regulation of several important mycobacterial pathogens creates the necessity to design simple and fast theoretical models that can predict them. This work proposes two DNA promoter QSAR models based on pseudo-folding lattice network (LN) and star-graphs (SG) topological indices. In addition, a comparative study with the previous RNA electrostatic parameters of thermodynamically-driven secondary structure folding representations has been carried out. The best model of this work was obtained with only two LN stochastic electrostatic potentials and it is characterized by accuracy, selectivity and specificity of 90.87%, 82.96% and 92.95%, respectively. In addition, we pointed out the SG result dependence on the DNA sequence codification and we proposed a QSAR model based on codons and only three SG spectral moments.
authors.affiliation: Department of Microbiology and Parasitology, University of Santiago de Compostela, Santiago de Compostela 15782, Spain. alcidopb@gmail.com
authors.forename: Alcides
authors.initials: A
authors.lastname: Perez-Bello
authors.forename: Cristian Robert
authors.initials: CR
authors.lastname: Munteanu
authors.forename: Florencio M
authors.initials: FM
authors.lastname: Ubeira
authors.forename: Alexandre Lopes
authors.initials: AL
authors.lastname: De Magalhães
authors.forename: Eugenio
authors.initials: E
authors.lastname: Uriarte
authors.forename: Humberto
authors.initials: H
authors.lastname: González-Díaz
mesh_terms: D003062:Codon; D004269:DNA, Bacterial / Q000235:genetics*; D008390:Markov Chains; D008954:Models, Biological; D009161:Mycobacterium / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017433:Protein Structure, Secondary; D021281:Quantitative Structure-Activity Relationship
chemical_list: D003062:Codon; D004269:DNA, Bacterial