Using iterative restart in finding subtle regulatory signals

Abstract

Biologists have determined that the control or regulation of gene expression is primarily determined by relatively short sequences in the region surrounding a gene. These sequences vary in length, position, redundancy, orientation, and bases. Finding these short sequences is a fundamental problem in molecular biology with important applications. Though there exist many different approaches to signal (i.e. short sequence) finding, some new study suggests that this problem still leaves plenty of room for improvement. In this paper, we report an improvement to our previously developed algorithm by adding an iterative restart strategy. We demonstrate the effectiveness of the synergy by comparing this new system with other algorithms on the Challenge Problem proposed by Peuzner and Sze.