Using Weeder for the discovery of conserved transcription factor binding sites

One of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder is a software package freely available for non commercial users as a stand-alone or Web-based application for the automatic discovery of conserved motifs in a set of related DNA sequences from coregulated genes. The motifs found are likely to represent instances of binding sites for some common transcription factor regulating the genes of the set. The program has been designed to make its usage as simple as possible and to require very little prior knowledge about the length and conservation of the motifs to be found.