Identification of DNA-protein Binding Sites through Multi-Scale Local Average Blocks on Sequence Information

Abstract

DNA-protein interactions appear as pivotal roles in diverse biological procedures and are paramount for cell metabolism, while identifying them with computational means is a kind of prudent scenario in depleting in vitro and in vivo experimental charging. A variety of state-of-the-art investigations have been elucidated to improve the accuracy of the DNA-protein binding sites prediction. Nevertheless, structure-based approaches are limited under the condition without 3D information, and the predictive validity is still refinable. In this essay, we address a kind of competitive method called Multi-scale Local Average Blocks (MLAB) algorithm to solve this issue. Different from structure-based routes, MLAB exploits a strategy that not only extracts local evolutionary information from primary sequences, but also using predicts solvent accessibility. Moreover, the construction about predictors of DNA-protein binding sites wields an ensemble weighted sparse representation model with random under-sampling. To evaluate the performance of MLAB, we conduct comprehensive experiments of DNA-protein binding sites prediction. MLAB gives MCC of 0.392, 0.315, 0.439 and 0.245 on PDNA-543, PDNA-41, PDNA-316 and PDNA-52 datasets, respectively. It shows that MLAB gains advantages by comparing with other outstanding methods. MCC for our method is increased by at least 0.053, 0.015 and 0.064 on PDNA-543, PDNA-41 and PDNA-316 datasets, respectively.