Skip Navigation



Nucleic Acids Research Advance Access published online on May 3, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn195
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4414K) Freely available
Right arrow Screen PDF (459K) Freely available
Right arrow Supplementary Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hooghe, B.
Right arrow Articles by De Bleser, P.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hooghe, B.
Right arrow Articles by De Bleser, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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.

Web Server Issue

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.