Discovery Biological Motifs Using Heuristics Approaches

Abstract

The identification of transcription factors binding sites (TFBS) – also called motifs – in DNA sequences is the first step to understanding how works gene regulation. Recognizing these patterns in the promoter regions of co-expressed genes is a determining key for this. Although there are several algorithms for this purpose, the problem is still far from being solved because of the great diversity of gene expression and the binding sites low specificity. State of the art algorithms have limitations, such as the high number of false positives and low accuracy for Identifying weak motifs. In this article we proposed a new approach based on memetic algorithms (DMMA) for discovery mofifs. The proposed approach was developed using evolutionary computation along with the local search algorithms simulated annealing and variable neighborhood search. To attest the algorithm ability, tests were conducted in four datasets - two real and two synthetic - and the results were compared with other approaches in the literature.