phiSITE: database of gene regulation in bacteriophages

Abstract

We have developed phiSITE, database of gene regulation in bacteriophages. To date it contains detailed information about more than 700 experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from 32 bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central) and stored in SQL based database system. The system provides full text search for regulatory elements, graphical visualization of phage genomes and several export options. In addition, visualizations of gene regulatory networks for five phages (Bacillus phage GA-1, Enterobacteria phage lambda, Enterobacteria phage Mu, Enterobacteria phage P2 and Mycoplasma phage P1) have been defined and made available. The phiSITE is accessible at http://www.phisite.org/.

Figure 1.

Result of a ‘Quick Search’ for all regulatory sites from Enterobacteria phage lambda. Each entry contains description of a site and links to other information resources. Three sites (PR', PFE and PRM) are selected and can be exported using the ‘Export selected’ button.

Figure 2.

Graphical applet zoomed to the region between Enterobacteria phage lambda genes cI and cro. User can use a mouse to zoom in/out and to scroll along the phage genome.