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Nucleic Acids Res. 2017 Jul 3;45(W1):W490-W494. doi: 10.1093/nar/gkx376.

ConTra v3: a tool to identify transcription factor binding sites across species, update 2017.

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VIB Bioinformatics Core, Rijvischestraat 126 3R, 9052 Zwijnaarde-Ghent, Belgium.
VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium.
Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium.
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, S9, 9000 Gent, Belgium.


Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes. In this updated version, with a completely re-implemented user interface using latest web technologies, users can choose from nine reference organisms ranging from human to yeast. ConTra v3 can analyze promoter regions, 5΄-UTRs, 3΄-UTRs and introns or any other genomic region of interest. Thousands of position weight matrices are available to choose from for detecting specific binding sites. Besides this visualization option, additional new exploration functionality is added to the tool that will automatically detect TFBSs having at the same time the highest regulatory potential, the highest conservation scores of the genomic regions covered by the predicted TFBSs and strongest co-localizations with genomic regions exhibiting regulatory activity. The ConTra v3 web server is freely available at

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