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Nucleic Acids Research, 2003, Vol. 31, No. 13 3589-3592
© 2003 Oxford University Press

Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors

Alona Sosinsky1,2, Christopher P. Bonin1, Richard S. Mann1 and Barry Honig*,1,2

1 Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, USA 2 Howard Hughes Medical Institute, New York, USA

*To whom correspondence should be addressed at Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, 630 W 168th Street, New York, NY 10032, USA. Tel: +1 2123057970; Fax: +1 2123056926; Email: bh6{at}columbia.edu

With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target_Explorer/


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