RSAT - matrix-scan

Scan a DNA sequence with a profile matrix

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

Sequence       Format Paste your sequence in the box below

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


Mask 

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

Prokaryotes

DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11) - [local copy]
RegulonDB prokaryotes - [93 motifs] (2015_08) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11066 motifs] (2018-06) - [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]

Pseudo-counts distributed in an equiprobable waydistributed proportionally to residues priors

Background model estimation method

    Markov order     High orders can be time-consuming, but order 0 is generally not representative. We recommend orders 1 or 2.
    Estimate residue probabilities from input sequences

    Organism-specific

      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

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

Pseudo-frequencies


Scanning options

Search strands      Origin     Offset   score decimals   handling of N characters

Return (Select one return type)


Individual matches

CRERs
(Cis-Regulatory element
Enriched Regions)

Enrichment of hits
in the whole input sequence set
Fields to
return







   sort by   
Other fields to return
Thresholds
Field Lower
Threshold
Upper
Threshold
Weight
score
P-value
Sig
P(S|M)
proba_M
P(S|B)
proba_B
Normalized
weight
Rank
Field Lower
Threshold
Upper
Threshold
CRER size*
site P-value*
CRER sites
CRER pval
CRER sig
* =mandatory field
Field Lower
Threshold
Upper
Threshold
Occurrences
Weight
score
Occurrences
above the score
Enrichment
Expected
occurrences
Occ P-value
Occ E-value
Occ sig
Rank


Output  
      MANUAL MAIL