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)


Mask 

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

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1532 motifs] (2018-04) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]
JASPAR core redundant plants - [501 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [10417 motifs] (2018-04) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]
JASPAR core redundant all - [1564 motifs] (2018) - [local copy]

RNA binding

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

Background

Background model estimation method

    Markov order  
    Estimate residue probabilities from input sequences

    Organism-specific

      Organism 
      [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
    Threshold
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

Output  
      MANUAL MAIL