Understanding the complex mechanisms governing basic biological processes requires the characterisation of regulatory motifs modulating gene expression at transcriptional and post-transcriptional level. In particular, extent, chronology and cell-specificity of transcription are modulated by the interaction of transcription factors with their corresponding binding sites, mostly located near (or sometimes quite far away from) the transcription start site of the gene. The constantly growing amount of genomic data, complemented by other sources of information such as expression data derived from microarray experiments, has opened new opportunities to researchers in this field. Many different methods have been proposed for the identification of transcription factor binding sites in the regulatory regions of co-expressed genes: unfortunately this is a very challenging problem both from the computational and the biological viewpoint. This paper provides a survey of existing methods proposed for the problem, focusing both on the ideas underlying them and their availability to the scientific community.