Some Implementation Issues of Heuristic Methods for Motif Extraction from DNA Sequences

Frequently, a set of conserved (common) motifs in a group of functionally related biological sequences (DNA/RNA or proteins) has a specific biological function. Determination of compact groups of these common patterns is a prerequisite for their efficient modeling. We discuss some of the most crucial aspects of computer implementation of three heuristic algorithms which can be used in computational extraction of such conserved motifs from a set of unaligned DNA/RNA sequences. The algorithms included are tabu search, simulated annealing and a population-based genetic algorithm. A server with these algorithms implemented is available as a public web application free for academic and non-profit users at http://sdmc.i2r.a-star.edu.sg/DRAGON/Motif_Search/ . This tool can be directly applied in determination of functional patterns in DNA and RNA.