COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS SEARCH FOR REGULATORY MOTIFS IN DROSOPHILA MELANOGASTER GENOME

Motivation: The major challenge in understanding genomic sequences is to reveal how spatio-temporal information on gene expression is encoded in the genome. Identification of regions on the genome that contain regulatory information is the first stage of this process. It is widely accepted that comparative sequence data can help in location of these regions in higher eucaryotic genomes. The inter-species comparison allows us to identify highly conserved regions on the genome that can contain clusters of binding sites for multiple transcription factors. Results: With published genomic sequences for Drosophila melanogaster and Drosophila pseudoobscura, we identified conserved regions on the genome that contain putative transcription factor binding sites. For the clusters of co-expressed genes found via microarray data analysis, we ran searches for statistically over-represented motifs in the corresponding groups of non-coding conserved sequences. These searches were carried out with SPEXS, which enumerates and scores all shared motifs in the sequences of unrestricted length. Availability: Sequence motif data is available from the authors