Submitted to the faculty of Indiana University in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, December 2004 / The process of generating RNA message from a gene is termed "transcription," and is performed by aptly named "transcription factors." These transcription factors can function singly or in conjunction with other factors to regulate gene expression, and thereby control, at one level, the amount of protein product which a gene can produce. This transcriptional regulation can have profound biological effects. Identification of the DNA sequences bound by transcription factors (regulatory elements) is a challenge as these sequences can be very short and may be located large distances from the target gene. Also, many current approaches for discovering regulatory elements in genomic DNA are limited to those sequences previously identified as consensus sequences for transcription factors. We have developed a novel tool, ReguLocator, for the identification of putative regulatory element. It uses the Smith-Waterman algorithm to identify short, conserved DNA sequences (ranked by p-value) derived from 2 large DNA sequences of interest. No weighting is applied for spatial alignment. Although speed must be improved to make use of ReguLocator practical, initial comparisons to similar tools provide promising results, and may open the door to better regulatory element identification.