SwissRegulon

SwissRegulon is a software tool that provides a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. This tool is a valuable resource for bioinformatics researchers interested in studying gene expression regulation. SwissRegulon contains annotations for yeast and 17 prokaryotic genomes, making it a useful tool for researchers working with various organisms. The annotations provided by SwissRegulon are produced using several recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes. The algorithms also utilize known sites from the literature and ChIP-on-chip binding data. In addition to providing information about the sequence, location, orientation, posterior probability, and binding factor of each annotated site, SwissRegulon also enables easy viewing of the regulatory site annotations in the context of other features annotated on the genomes. This is achieved using the GBrowse genome browser interface, which allows researchers to visualize the regulatory sites in the context of other genomic features. This feature of SwissRegulon is particularly useful for researchers interested in studying the regulation of gene expression in a particular region of the genome. SwissRegulon also offers the ability to query the database for regulons, i.e., sites bound by a common factor. This feature is particularly useful for researchers interested in identifying the regulatory networks that control gene expression in a particular organism.