Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices

• Type: Another Publication in an International Scientific Journal
• Date: 2009

Authors

Alcides Perez Bello (Author) Other; Cristian Robert Munteanu (Author) Other; Florencio M Ubeira (Author) Other; Alexandre Lopes De Magalhaes (Author) FCUP; Eugenio Uriarte (Author) Other; Humberto Gonzalez Diaz (Author) Other

Journal

Title: Journal of Theoretical Biology

Vol. 256

Pages: 458-466

ISSN: 0022-5193

Publisher: Elsevier

Indexing

ISI Web of Knowledge - 44 Citations

Scopus - 44 Citations

Scientific classification

FOS: Natural sciences > Mathematics

Other information

Authenticus ID: P-003-N7F

DOI: 10.1016/j.jtbi.2008.09.035

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 9