RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

RegulonDB is a database on mechanisms of transcription regulation and opero n organization in Escherichia coli K-12. The current version has considerab ly increased numbers of regulatory elements such as promoters, binding site s and terminators. The complete repertoire of known and predicted DNA-bindi ng transcriptional regulators can be considered to be included in this vers ion. The database now distinguishes different allosteric conformations of r egulatory proteins indicating the one active in binding and regulating the different promoters. A new set of operon predictions has been incorporated. The relational design has been modified accordingly. Furthermore, a major improvement is a graphic display enabling browsing of the database with a J ava-based graphic user interface with three zoom-levels connected to proper ties of each chromosomal element. The purpose of these modifications is to make RegulonDB a useful tool and control set for transcriptome experiments. RegulonDB can be accessed on the web at the URL: http:www.cifn.unam.mx/Com putational-Biology/regulondb/.