RSAT : matrix-scan

RSAT - matrix-scan

Scan DNA sequences with position-specific scoring matrices (PSSM)

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 use motif consensus as matrix name

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)

Input

1 - Select a database in list:

2 - Select a collection in list:

3 - Select one or more matrix identifiers:

View matrix descriptions & download full collections

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

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

Input your own background file

Format

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

sites pval rank
limits normw
weight_limits
bg_residues

crer normw
limits sites
crer-specific identifiers

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
Enrichment
Expected occurrences
Occ P-value
Occ E-value
Occ sig
Rank

Output displayemail

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