EREFinder: Genome-wide detection of estrogen response elements

Motivation Estrogen response elements (EREs) are specific DNA sequences to which ligand-bound estrogen receptors (ERs) physically bind, allowing them to act as transcription factors for target genes. Locating EREs and ER responsive regions is therefore a potentially important component of the study of estrogen-regulated pathways. Results We tested and demonstrated the ability of EREFinder, a novel algorithm we developed, to locate regions of ER-binding across the human genome and show that these regions designated by the program occur more frequently near estrogen responsive genes. EREFinder can handle large input files, has settings to allow for broad and narrow searches, and provides the full output to allow for greater data manipulation. These features facilitate a wide range of hypothesis testing for researchers and make EREFinder an excellent tool to aid in estrogen-related research. Availability and Implementation Source code and binaries freely available for download at https://github.com/JonesLabIdaho/EREfinder , implemented in C++ and supported on Linux and MS Windows. Contact [email protected] Supplemental Materials R scripts can be found at https://github.com/JonesLabIdaho/EREfinder