question: Which are the most widely used computational methods for the identification of CRMs (cis-regulatory modules)?
answer: Computational methods attempting to identify instances of cis-regulatory modules (CRMs) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions involved remains limited. When discriminating CRMs from non-coding regions, those methods considering evolutionary conservation have a stronger predictive power than methods designed to be run on a single genome. Furthermore, most methods appear to be sensitive to the composition and structure of the genome to which they are applied. CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs.