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Nucleic Acids Research Advance Access published online on May 3, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn195
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

Bart Hooghe1,2,3,*, Paco Hulpiau1,2,3, Frans van Roy2,3 and Pieter De Bleser1,2,3

1Bioinformatics Core Facility, VIB, 2Department of Molecular Biology, Ghent University and 3Department for Molecular Biomedical Research, VIB, B-9052 Ghent, Belgium

*To whom correspondence should be addressed. Tel: 003293313693; Email: bart.hooghe{at}dmbr.ugent.be

Received January 31, 2008. Revised March 28, 2008. Accepted April 2, 2008.

Transcription factors (TFs) are key components in signaling pathways, and the presence of their binding sites in the promoter regions of DNA is essential for their regulation of the expression of the corresponding genes. Orthologous promoter sequences are commonly used to increase the specificity with which potentially functional transcription factor binding sites (TFBSs) are recognized and to detect possibly important similarities or differences between the different species. The ConTra (conserved TFBSs) web server provides the biologist at the bench with a user-friendly tool to interactively visualize TFBSs predicted using either TransFac (1) or JASPAR (2) position weight matrix libraries, on a promoter alignment of choice. The visualization can be preceded by a simple scoring analysis to explore which TFs are the most likely to bind to the promoter of interest. The ConTra web server is available at http://bioit.dmbr.ugent.be/ConTra/index.php.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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