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Nucleic Acids Research, 2003, Vol. 31, No. 13 3605-3607
© 2003 Oxford University Press

Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes

Vladimir B. Bajic*, Sin Lam Tan, Allen Chong, Suisheng Tang, Anders Ström1, Jan-Åke Gustafsson2, Chin-Yo Lin3 and Edison T. Liu3

Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613 1 Center for Biotechnology, Karolinska Institute, Novum, S-141 57 Huddinge, Sweden 2 Department of Medical Nutrition, Karolinska Institute, Novum, S-141 57 Huddinge, Sweden 3 Genome Institute of Singapore, Singapore 117528

*To whom correspondence should be addressed. Tel: +65 68748800; Fax: +65 67748056; Email: bajicv{at}i2r.a-star.edu.sg

We present a unique program for identification of estrogen response elements (EREs) in genomic DNA and related analyses. The detection algorithm was tested on several large datasets and makes one prediction in 13 300 nt while achieving a sensitivity of 83%. Users can further investigate selected regions around the identified ERE patterns for transcription factor binding sites based on the TRANSFAC database. It is also possible to search for candidate human genes with a match for the identified EREs and their flanking regions within EPD annotated promoters. Additionally, users can search among the extended promoter regions of ~11 000 human genes for those that have a high degree of similarity to the identified ERE patterns. Dragon ERE Finder version 2 is freely available for academic and non-profit users (http://sdmc.lit.org.sg/ERE-V2/index).


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