RSAT - dyad-analysis
Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences
Reference: van Helden, J., Rios, A. F. and Collado-Vides, J. (2000). Nucleic Acids Res 28, 1808-18.
Warning !! For
vertebrate genomes, analyses of complete promoters from
co-expressed gene groups return
many false positive (i.e. if you submit a random set of genes, you always get plenty of highly 'significant' motifs). This is likely to come from the heterogeneity of human sequences (mixtures of GC-rich and GC-poor promoters).
However, analyses of
ChIP-seq peaks return
very good results. See the program
peak-motifs.
