RSAT - matrix-quality

Evaluate the quality of a Position-Specific Scoring Matrix (PSSM), by comparing the empirical distributions obtained in various sequence sets.

The most classical use of the program is to compare score distributions between positive sequences (e.g. true binding sites for the considered transcription factor) and negative sequences (e.g. intergenic sequences between convergently transcribed genes).

Program developed by Alejandra Medina Rivera, Morgane Thomas-Chollier, and Jacques van Helden.

Citation: Medina-Rivera, A., Abreu-Goodger, C., Salgado-Osorio, H., Collado-Vides, J. and van Helden, J. (2010). Empirical and theoretical evaluation of transcription factor binding motifs. Nucleic Acids Res. 2010 Oct 4. [Epub ahead of print] [Pubmed 20923783] [Full text].

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)

Input1 - Select a database in list:
2 - Select a collection in list:
3 - Select one or more matrix identifiers:

View matrix descriptions & download full collections

Fungi

JASPAR core nonredundant fungi - [0 motifs] (2020) - [local copy]
JASPAR core redundant fungi - [0 motifs] (2020) - [local copy]
Yeastract s_cerevisiae - [0 motifs] (20130918) - [local copy]
cisBP Saccharomyces_cerevisiae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP s_cerevisiae - [0 motifs] (2015-06_v1.02) - [local copy]

Multi-organisms

JASPAR unvalidated - [0 motifs] (2020) - [local copy]
JASPAR core redundant all - [0 motifs] (2020) - [local copy]
JASPAR core nonredundant all - [0 motifs] (2020) - [local copy]
footprintDB all - [11842 motifs] (2020-01) - [local copy]
RSAT non-redundant insects+plants+vertebrates - [0 motifs] (2017) - [local copy]

Non-vertebrate Metazoa

DrosophilaTFs - [0 motifs] (2015-11) - [local copy]
Drosophila IDMMPMM - [0 motifs] (2010_11) - [local copy]
Drosophila DMMPMM - [0 motifs] (2010_11) - [local copy]
JASPAR core nonredundant urochordates - [0 motifs] (2020) - [local copy]
JASPAR core redundant urochordates - [0 motifs] (2020) - [local copy]
JASPAR core redundant nematodes - [0 motifs] (2020) - [local copy]
JASPAR core redundant insects - [0 motifs] (2020) - [local copy]
JASPAR core nonredundant nematodes - [0 motifs] (2020) - [local copy]
JASPAR core nonredundant insects - [0 motifs] (2020) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7464 motifs] (2020-01) - [local copy]
RSAT non-redundant insects - [0 motifs] (2017) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [0 motifs] (2016_06) - [local copy]
cisBP Caenorhabditis_briggsae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_brenneri - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Culex_quinquefasciatus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_darlingi - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Onchocerca_volvulus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Tetranychus_urticae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_pseudoobscura - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Schistosoma_mansoni - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_simulans - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_mojavensis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Crassostrea_gigas - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_persimilis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Octopus_bimaculoides - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_melanogaster - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_gambiae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichoplax_adhaerens - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Lucilia_cuprina - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Apis_mellifera - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_erecta - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Strongylocentrotus_purpuratus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP drosophila - [0 motifs] (2014-10_v0.9) - [local copy]
cisBP Heliconius_melpomene - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichinella_spiralis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Zootermopsis_nevadensis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Tribolium_castaneum - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_yakuba - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Acyrthosiphon_pisum - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Melitaea_cinxia - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_willistoni - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brugia_malayi - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Loa_loa - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Daphnia_pulex - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Strigamia_maritima - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Amphimedon_queenslandica - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Solenopsis_invicta - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Ixodes_scapularis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Rhodnius_prolixus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Lottia_gigantea - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Megaselia_scalaris - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Atta_cephalotes - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Pediculus_humanus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_japonica - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_sechellia - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP c_elegans - [0 motifs] (2015-05_v1.02) - [local copy]
cisBP Dendroctonus_ponderosae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_virilis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Ciona_intestinalis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Danaus_plexippus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_ananassae - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Bombyx_mori - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_remanei - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Aedes_aegypti - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_elegans - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Pristionchus_pacificus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_grimshawi - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Helobdella_robusta - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Nasonia_vitripennis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Nematostella_vectensis - [0 motifs] (2019-06_v2.00) - [local copy]

Plants

ArabidopsisPBM (A thaliana) - [0 motifs] (2015-11) - [local copy]
JASPAR core redundant plants - [0 motifs] (2020) - [local copy]
JASPAR core nonredundant plants - [0 motifs] (2020) - [local copy]
Athamap (A thaliana) - [0 motifs] (2015-11) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1878 motifs] (2020-01) - [local copy]
RSAT non-redundant plants - [0 motifs] (2017) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [0 motifs] (2016-06) - [local copy]
cisBP Oryza_rufipogon - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brachypodium_distachyon - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_persica - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Vitis_vinifera - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_rapa - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP a_thaliana - [0 motifs] (2015-06_v1.02) - [local copy]
cisBP Leersia_perrieri - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_brachyantha - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_oleracea - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Musa_acuminata - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Sorghum_bicolor - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glaberrima - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_sativa - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_tuberosum - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Medicago_truncatula - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Setaria_italica - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_mume - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_barthii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Ostreococcus_lucimarinus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Gossypium_raimondii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_urartu - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Manihot_esculenta - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glumaepatula - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_nivara - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlamydomonas_reinhardtii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Glycine_max - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_napus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_punctata - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Helianthus_annuus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_lycopersicum - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Zea_mays - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Selaginella_moellendorffii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_indica - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Cucumis_sativus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Hordeum_vulgare - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Physcomitrella_patens - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Populus_trichocarpa - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_longistaminata - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Aegilops_tauschii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Fragaria_vesca - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Amborella_trichopoda - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_aestivum - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_meridionalis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Arabidopsis_lyrata - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Phaseolus_vulgaris - [0 motifs] (2019-06_v2.00) - [local copy]

Prokaryotes

DBTBS (Bacillus Subtilis) - [0 motifs] (2015-11) - [local copy]
RegulonDB prokaryotes - [0 motifs] (2015_08) - [local copy]

RNA binding

RBPDB - [0 motifs] (2017) - [local copy]
ATtRACT - [0 motifs] (2017) - [local copy]
CISBP-RNA - [0 motifs] (2017) - [local copy]

Vertebrates

Homer (Human TF motifs) - [0 motifs] (2016-07) - [local copy]
Methylated motifs HCT116 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs H1-hESC (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs GM12878 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs SK-N-SH (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs IMR-90 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs A549 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs HepG2 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs SNU398 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs HeLa-S3 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs HEK293 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs HEK293T (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs K562 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Methylated motifs MCF-7 (Human TFs) - [0 motifs] (2018-11) - [local copy]
Hocomoco (Mouse TFs) - [0 motifs] (2017-10) - [local copy]
Hocomoco (Human TFs) - [0 motifs] (2017-10) - [local copy]
hPDI (Human TFs identified by protein microarray assays) - [0 motifs] (2016-06) - [local copy]
HT-Selex (Human TFs) - [0 motifs] (2018-03) - [local copy]
HT-Methyl-Selex (Human TFs) - [0 motifs] (2018-03) - [local copy]
ENCODE (Human TFs) - [0 motifs] (2018-03) - [local copy]
JASPAR core nonredundant vertebrates - [0 motifs] (2020) - [local copy]
JASPAR core redundant vertebrates - [0 motifs] (2020) - [local copy]
RSAT non-redundant vertebrates - [0 motifs] (2017) - [local copy]
Jolma_2013 (Human TFs) - [0 motifs] (2015-11) - [local copy]
Human_TF_dimers (Human TFs dimers) - [0 motifs] (2016-05) - [local copy]
cisBP Echinops_telfairi - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Mus_musculus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Erinaceus_europaeus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP mouse - [0 motifs] (2014-10_v0.9) - [local copy]
cisBP Dipodomys_ordii - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Cavia_porcellus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Equus_caballus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlorocebus_sabaeus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP human - [0 motifs] (2014-10_v0.9) - [local copy]
cisBP Bos_taurus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Astyanax_mexicanus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Rattus_norvegicus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Homo_sapiens - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Danio_rerio - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Gallus_gallus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Ailuropoda_melanoleuca - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Dasypus_novemcinctus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Callithrix_jacchus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Anas_platyrhynchos - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Oreochromis_niloticus - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Xenopus_tropicalis - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Choloepus_hoffmanni - [0 motifs] (2019-06_v2.00) - [local copy]
Epigram (Human Histone marks related motifs) - [0 motifs] (2016-06) - [local copy]
NCAP-SELEX (HUMAN TFs) - [0 motifs] (2018-09) - [local copy]
CAP-SELEX - [0 motifs] (2018-09) - [local copy]

ZF_ChIP-exo

2020-07 - [0 motifs] (https://www.biorxiv.org/content/10.1101/630756v4) - [local copy]

ZF_ChIP-seq

2020-07 - [0 motifs] (https://www.biorxiv.org/content/10.1101/630756v4) - [local copy]

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

 Matrix file includes sites

Only the first matrix will be taken in acount

K fold validation      Note: validation requires a matrix with binding sites, in a suitable format (e.g. transfac, meme).

2 - Sequences

Mandatory Sequence

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 

    Number of matrix permutations    separate permutations

    Tag for this data set

 Calculate NWD

Optional Sequence

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 

    Number of matrix permutations    separate permutations

    Tag for this data set

 Calculate NWD

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

      Genomes in the RSAT Prokaryotes server were recently re-installed. Genome names now follow the NCBI standard to easily identify assemblies, if you cannot find your genome please check this naming list to find the correct ID: Genome IDs list

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

Pseudo-frequencies

Output  

      [Sample Output] MANUAL