Optimizing genetic algorithm for motif discovery

Planted (l,d)(l,d)-motif identification is an important and challenging problem in computational biology. In this paper, we present an original algorithm (GARPS) that combines Genetic Algorithm (GA) and Random Projection Strategy (RPS) to identify (l,d)(l,d)-motifs. We start with RPS to find good starting positions by introducing position-weighted function and hash each of all ll-mers in the input sequences onto the corresponding kk-dimensional (k