RSA-tools - matrix-scan

Scan a DNA sequence with a profile matrix
Program developed by Jean Valéry Turatsinze, Morgane Thomas-Chollier and Jacques van Helden

Sequence       Format Mask 
Paste your sequence in the box below

Or select a file to upload


Matrix (or matrices)        Format  use motif consensus as matrix name

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

Background model
Markov Chain order     High orders can be time-comsuming.

Estimation method
Estimate from input sequences
Sliding window  
Genome subset   Organism 
Upload your own file for the background model     
    Format 

Pseudo-frequencies

Scanning options

Search strands      Origin     score decimals

Return (Select one return type)


Individual matches
CRERs
(Cis-Regulatory element
Enriched Regions)
Over-representation of hits
in the whole input sequence set
Fields to
return		 sites pval rank
limits normw
weight_limits
bg_residues
crer normw
limits sites
crer identifier 		distrib
occ_proba    sort by   
Other fields to return matrix freq_matrix weight_matrix bg_model
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
Over-representation
Expected
occurrences
Occ P-value
Occ E-value
Occ sig
Rank

Output displayemail