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 

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

Background model estimation method

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