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Open Access Software

P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes

Mohamed Barakat123*, Philippe Ortet123 and David E Whitworth4

Author Affiliations

1 CEA, DSV, IBEB, SBVME, LEMiRE, Saint-Paul-lez-Durance, F-13108, France

2 CNRS, UMR 7265, Saint-Paul-lez-Durance, F-13108, France

3 Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France

4 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK

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BMC Genomics 2013, 14:269  doi:10.1186/1471-2164-14-269

Published: 20 April 2013

Abstract

Background

Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences.

Results

We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats.

Conclusion

Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users’ sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org webcite.