RSAT - dyad-analysis

Analysis of spaced dyads in a set of DNA 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)


Mask 
 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     

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

    Taxon 

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


Return

Fields Lower
Threshold
Upper
Threshold
 Convert assembled patterns to matrices.
            Max matrices    Min site weight    Flanking residues

Output 
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