PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

Abstract

PRODORIC is a database that provides annotated information on the regulation of gene expression in prokaryotes. It integrates a large compilation of gene regulatory data including transcription factor binding sites, promoter structures and gene expression patterns. The whole dataset is manually curated and relies on published results extracted from the scientific literature. The current extended version of PRODORIC contains gene regulatory data for several new microorganisms. Major improvements were realized in the design of the web interface and the accessibility of the stored information. The database was further improved by the implementation of various new tools for the elucidation of gene regulatory interactions. Thus, the PRODORIC platform represents a framework for the interactive exploration, prediction and evaluation of gene regulatory networks in prokaryotes. PRODORIC is accessible at http://www.prodoric.de.

Figure 1.

Position weight matrix view of PRODORIC for the binding site of the Anr transcription faction from Pseudomonas aerugionosa.

Figure 2.

SMILE analysis using the Anr binding site in the promoter of the hemN gene. The results show both a high evolutional and positional conservation between the orthologous promoters (the list of matches was shortened).