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Position frequency matrices (PFMs) represent the most widely employed model for transcription factor binding motifs (TFBMs). Given a set of TFBMs, regulatory networks can be predicted through in silico methods by using cognate binding sequences to construct models. The availability of PFMs offers much promise for high throughput TFBM detection in the form of a pipeline to facilitate the analysis of microarray data. Here we present BiSAn, a simple yet effective software for biologists to efficiently identify putative TFBMs from promoter sites belonging to their genes of interest at the click of a button. BiSAn is freely available and can be downloaded from http://www.1066technologies.co.uk/bisan.