RSAT - matrix-scan QUICK and SIMPLE

Scan a DNA sequence with a profile matrix
This quick version was programmed by Matthieu Defrance, Web interface by Morgane Thomas-Chollier
Citation: Jean Valéry Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance and Jacques van Helden (2008).
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc, 3, 1578-1588. Pubmed 18802439

--> Click here to access the ADVANCED form <-- (custom background, CRER detection, overrepresentation of sites,...)
Sequences      Paste your sequence (fasta format)

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

   URL of a sequence file available on a Web server (e.g. Galaxy).


Matrix Matrix (or matrices)        Format 

Or select a file to upload


Background model estimation method

    Markov order  
    Estimate residue probabilities from input sequences


      Organism  not seeing your favorite organism in the list ? Contact us to have it installed
      Sequence type  

Scanning options    Sequence Origin
    Return   Calculating pval is slighly slower
weight score >=if return is 'sites only', the threshold is set on the weight score
pval <=if return is 'sites + pval ', the threshold is set on the pval