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Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate
Vladimir B Bajic1, Sin Lam Tan, Allen Chong
1Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613. bajicv@i2r.a-star.edu.sg
Abstract:
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 approximately 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).