RSAT - matrix-enrichment

Evaluate the enrichment of a set of motifs in one or several sequence sets. (The web version only allows for four sequence sets)

The most classical use of the program is to indentify transcription factor binding sites that could be enriched or depleted in one or several sequence sets.

Program developed by Jaime A Castro-Mondragon, Samuel Collombet, Alejandra Medina-Rivera, Morgane Thomas-Chollier, and Jacques van Helden.


Title

1 - 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)


View matrix descriptions & download full collections

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1739 motifs] (2018-05) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]
JASPAR core redundant plants - [501 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11066 motifs] (2018-05) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]
JASPAR core redundant all - [1564 motifs] (2018) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]

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

Only the first 50 matrices will be taken into acount

2 - Sequences

Mandatory Sequence Set

Dataset 1     Paste your sequence (fasta format)

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

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

    Tag for this data set

Optional Sequence Set 1

Dataset 2     Paste your sequence (fasta format)

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

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

    Tag for this data set

Optional Sequence Set 2

Dataset 3     Paste your sequence (fasta format)

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

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

    Tag for this data set

Optional Sequence Set 3

Dataset 4     Paste your sequence (fasta format)

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

   URL of a sequence file available on a Web server (e.g. Galaxy).


Mask 

    Tag for this data set

3 - Background

Background model estimation method

    Markov order     High orders can be time-consuming, but order 0 is generally not representative. We recommend orders 1 or 2.

    Organism-specific

      Organism 
      [List of organisms] not seeing your favorite organism in the list ? Contact us to have it installed
      Sequence type  

Pseudo-frequencies

Output  

      MANUAL