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Nucleic Acids Research Advance Access published online on November 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp911
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

phiSITE: database of gene regulation in bacteriophages

Lubos Klucar*, Matej Stano and Matus Hajduk

Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84551 Bratislava, Slovakia

*To whom correspondence should be addressed. Tel: +421 2 5930 7413; Fax: +421 2 5930 7416; Email: lubos.klucar{at}savba.sk

Received August 15, 2009. Accepted October 7, 2009.

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/.


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