erefinder: Genome-wide detection of oestrogen response elements

Oestrogen response elements (EREs) are specific DNA sequences to which ligand-bound oestrogen 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 oestrogen-regulated pathways. Here, we report the development of a novel software tool, erefinder, which conducts a genome-wide, sliding-window analysis of oestrogen receptor binding affinity. We demonstrate the effects of adjusting window size and highlight the program's general agreement with ChIP studies. We further provide two examples of how erefinder can be used for comparative approaches. 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 oestrogen-related research.