RSA-tools : 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 use motif consensus as matrix name

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

Markov order

High orders can be time-consuming.

Estimate from input sequences

Sliding window

Organism-specific

Organism

Sequence type

Format

Pseudo-frequencies

Scanning options

Search strands Origin Offset score decimals handling of N characters

Return (Select one return type)

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

Output displayemail

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