The identification of regulatory motifs is important for the study ofthe regulation of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs sampling-based program for predicting regulatory motifs from co-regulataed genes in prokaryotes or lower eukaryotes ; (ii) CompareProspector, an extension to BioProspector which incorporates comparative genomics features to be used for higher eukaryotes ; (iii) MDscan, a program for finding protein-DNA interaction sites from ChIP-on-chip targets . All three programs examine a group of sequences that may share common regulatory motifs and output a list of putative motifs as position-specific probability matrices, the individual sites used to construct the motifs, and the location of each site on the input sequences. The web servers and executables can be accessed at http://seqmotifs.stanford.edu.
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