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.

Sequence       Format Paste your sequence in the box below

Or select a file to upload (.gz compressed files supported)

 purge sequences (highly recommended)

Dyad counting mode
Monad length  Spacing   from  to 
Dyad type 
Count on        prevent overlapping matches

Background model 

Genome subset  Sequence type     

    Genomes in the RSAT Prokaryotes server were recently re-installed. Genome names now follow the NCBI standard to easily identify assemblies, if you cannot find your genome please check this naming list to find the correct ID: Genome IDs list

    [List of organisms] not seeing your favorite organism in the list ? Contact us to have it installed

    Taxon  [List of taxonomy]

Monad frequencies from the input sequence
Upload your own expected frequency file


Fields Lower
 Convert assembled patterns to matrices.
            Max pattern assemblies    Min site weight    Flanking residues    Matrix clustering