Gene expression is governed by a number of regulatory sites and mechanisms, many of which are still unknown or poorly studied. Regulatory sites are more difficult to predict and study than genes, because they are short, variable, and change faster than coding regions during evolution. A comparative analysis of short regulatory sites, including prokaryotic cis-regulatory sites, will be performed using the genomic DNA sequences from a wide range of species. The project will develop new methods for predicting sites based on inherent statistical properties of sequence data and on conservation of sequence across species, using the sequences of closely related species to improve prediction. These methods will be applied to multiple bacterial, plant, and animal genomes and the results made available via a website as well as available to the community in the form of the new software and databases. The research will provide insights into comparative characteristic of regulatory sites in different genomes and can also be used to improve gene prediction software.
