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 Sequence       Format Paste your sequence in the box below

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


Matrix Matrix (or matrices)        Format 

Or select a file to upload

Or Dynamic selection of motifs from the available collections
(select the collection and a dropdown menu will appear to select motifs)

View matrix descriptions & download full collections


Yeastract s_cerevisiae - [732 motifs] (20130918) - [local copy]
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
cisBP Saccharomyces_cerevisiae - [1288 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant fungi - [183 motifs] (2020) - [local copy]
JASPAR core redundant fungi - [184 motifs] (2020) - [local copy]


RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11145 motifs] (2019-07) - [local copy]
JASPAR core nonredundant all - [1646 motifs] (2020) - [local copy]
JASPAR core redundant all - [1964 motifs] (2020) - [local copy]
JASPAR unvalidated - [337 motifs] (2020) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]


Background model estimation method

    Markov order  
    Estimate residue probabilities from input sequences


      [List of organisms] 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