RSAT : matrix-scan QUICK and SIMPLE

RSAT - matrix-scan QUICK and SIMPLE

Scan DNA sequences with position-specific scoring matrices (PSSM) - fast and simplified version
This quick version was programmed by Matthieu Defrance, Web interface by Morgane Thomas-Chollier

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

--> Click here to access the ADVANCED form <-- (custom background, CRER detection, overrepresentation of sites,...)

Sequences Sequence Format Paste your sequence in the box below

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

Mask

Matrix 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)

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

Background

Background model estimation method

Markov order

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

Scanning options    Sequence Origin
    Return   Calculating pval is slighly slower
    Threshold

weight score >=		if return is 'sites only', the threshold is set on the weight score
pval <=		if return is 'sites + pval* ', the threshold is set on the pval*

Output display

MANUAL

MAIL

RSAT - matrix-scan QUICK and SIMPLE

Fungi

Multi-organisms

Non-vertebrate Metazoa

Plants

Prokaryotes

RNA binding

Vertebrates