Mining the Database of Transcription Binding Sites

In this paper, we study the problems of motif discovery and gene regulation. First, although the sliding window technique based on profiles or consensus sequences is a standard method for discovering motifs in the genomes with prior knowledge of transcription binding sites in orthologous genes from related organisms, it usually has high computational costs. In this paper, we propose an efficient approximation method employing randomized algorithms to identify motifs. The approximation method can be easily combined with the sliding-window technique for efficient and accurate motif discovery. Second, we mine frequent motif combinations and sequential motif patterns to investigate the regulatory relationships between motifs and provide a better understanding of gene expression, regulation, and transcription