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

@article{citeulike:2761624, abstract = {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. 10.1093/nar/gkn195}, author = {Hooghe, Bart and Hulpiau, Paco and van Roy, Frans and De Bleser, Pieter }, citeulike-article-id = {2761624}, doi = {10.1093/nar/gkn195}, journal = {Nucl. Acids Res.}, keywords = {conserved, promoter, tool, transcription-factor}, month = {May}, pages = {gkn195+}, posted-at = {2008-05-13 10:38:49}, priority = {3}, title = {ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species}, url = {http://dx.doi.org/10.1093/nar/gkn195}, year = {2008} }

TY - JOUR ID - citeulike:2761624 L3 - citeulike-article-id:2761624 TI - ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species JF - Nucl. Acids Res. SP - gkn195 N2 - 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. 10.1093/nar/gkn195 KW - conserved KW - promoter KW - tool KW - transcription-factor AU - Hooghe, Bart AU - Hulpiau, Paco AU - van Roy, Frans AU - De Bleser, Pieter PY - 2008/05/03/ UR - http://dx.doi.org/10.1093/nar/gkn195 ER -