RSAT - matrix-quality

Evaluate the quality of a Position-Specific Scoring Matrix (PSSM), by comparing score distributions obtained with this matrix 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)


View matrix descriptions & download full collections

Vertebrates

ENCODE (Human TFs) - [2065 motifs] (2018-03) - [local copy]
HT-Methyl-Selex (Human TFs) - [923 motifs] (2018-03) - [local copy]
HT-Selex (Human TFs) - [864 motifs] (2018-03) - [local copy]
Hocomoco (Human TFs) - [771 motifs] (2017-10) - [local copy]
Hocomoco (Mouse TFs) - [531 motifs] (2017-10) - [local copy]
Homer (Human TF motifs) - [332 motifs] (2016-07) - [local copy]
Jolma_2013 (Human TFs) - [818 motifs] (2015-11) - [local copy]
Human_TF_dimers (Human TFs dimers) - [664 motifs] (2016-05) - [local copy]
Methylated motifs A549 (Human TFs) - [21 motifs] (2018-11) - [local copy]
Methylated motifs GM12878 (Human TFs) - [60 motifs] (2018-11) - [local copy]
Methylated motifs H1-hESC (Human TFs) - [35 motifs] (2018-11) - [local copy]
Methylated motifs HCT116 (Human TFs) - [16 motifs] (2018-11) - [local copy]
Methylated motifs HEK293 (Human TFs) - [88 motifs] (2018-11) - [local copy]
Methylated motifs HEK293T (Human TFs) - [9 motifs] (2018-11) - [local copy]
Methylated motifs HeLa-S3 (Human TFs) - [31 motifs] (2018-11) - [local copy]
Methylated motifs HepG2 (Human TFs) - [66 motifs] (2018-11) - [local copy]
Methylated motifs IMR-90 (Human TFs) - [11 motifs] (2018-11) - [local copy]
Methylated motifs K562 (Human TFs) - [108 motifs] (2018-11) - [local copy]
Methylated motifs MCF-7 (Human TFs) - [52 motifs] (2018-11) - [local copy]
Methylated motifs SK-N-SH (Human TFs) - [21 motifs] (2018-11) - [local copy]
Methylated motifs SNU398 (Human TFs) - [1 motifs] (2018-11) - [local copy]
NCAP-SELEX (HUMAN TFs) - [0 motifs] (2018-09) - [local copy]
RSAT non-redundant vertebrates - [2233 motifs] (2017) - [local copy]
cisBP Ailuropoda_melanoleuca - [5863 motifs] (2019-06_v2.00) - [local copy]
cisBP Anas_platyrhynchos - [5038 motifs] (2019-06_v2.00) - [local copy]
cisBP Astyanax_mexicanus - [5191 motifs] (2019-06_v2.00) - [local copy]
cisBP Bos_taurus - [5895 motifs] (2019-06_v2.00) - [local copy]
cisBP Callithrix_jacchus - [6089 motifs] (2019-06_v2.00) - [local copy]
cisBP Cavia_porcellus - [5683 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlorocebus_sabaeus - [6176 motifs] (2019-06_v2.00) - [local copy]
cisBP Choloepus_hoffmanni - [4069 motifs] (2019-06_v2.00) - [local copy]
cisBP Danio_rerio - [5320 motifs] (2019-06_v2.00) - [local copy]
cisBP Dasypus_novemcinctus - [5871 motifs] (2019-06_v2.00) - [local copy]
cisBP Dipodomys_ordii - [4810 motifs] (2019-06_v2.00) - [local copy]
cisBP Echinops_telfairi - [4813 motifs] (2019-06_v2.00) - [local copy]
cisBP Equus_caballus - [5765 motifs] (2019-06_v2.00) - [local copy]
cisBP Erinaceus_europaeus - [4783 motifs] (2019-06_v2.00) - [local copy]
cisBP Gallus_gallus - [5272 motifs] (2019-06_v2.00) - [local copy]
cisBP Homo_sapiens - [6607 motifs] (2019-06_v2.00) - [local copy]
cisBP Mus_musculus - [6014 motifs] (2019-06_v2.00) - [local copy]
cisBP Oreochromis_niloticus - [5296 motifs] (2019-06_v2.00) - [local copy]
cisBP Rattus_norvegicus - [5946 motifs] (2019-06_v2.00) - [local copy]
cisBP Xenopus_tropicalis - [5393 motifs] (2019-06_v2.00) - [local copy]
cisBP human - [1832 motifs] (2014-10_v0.9) - [local copy]
cisBP mouse - [1715 motifs] (2014-10_v0.9) - [local copy]
Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06) - [local copy]
hPDI (Human TFs identified by protein microarray assays) - [437 motifs] (2016-06) - [local copy]
JASPAR core nonredundant vertebrates - [579 motifs] (2018) - [local copy]
JASPAR core redundant vertebrates - [719 motifs] (2018) - [local copy]

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [652 motifs] (2016_06) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
cisBP Acyrthosiphon_pisum - [4022 motifs] (2019-06_v2.00) - [local copy]
cisBP Aedes_aegypti - [3985 motifs] (2019-06_v2.00) - [local copy]
cisBP Amphimedon_queenslandica - [2325 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_darlingi - [3542 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_gambiae - [4089 motifs] (2019-06_v2.00) - [local copy]
cisBP Apis_mellifera - [4133 motifs] (2019-06_v2.00) - [local copy]
cisBP Atta_cephalotes - [3404 motifs] (2019-06_v2.00) - [local copy]
cisBP Bombyx_mori - [3662 motifs] (2019-06_v2.00) - [local copy]
cisBP Brugia_malayi - [3105 motifs] (2019-06_v2.00) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP Caenorhabditis_brenneri - [3169 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_briggsae - [3261 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_elegans - [3438 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_japonica - [3107 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_remanei - [3289 motifs] (2019-06_v2.00) - [local copy]
cisBP Ciona_intestinalis - [3788 motifs] (2019-06_v2.00) - [local copy]
cisBP Crassostrea_gigas - [4030 motifs] (2019-06_v2.00) - [local copy]
cisBP Culex_quinquefasciatus - [3982 motifs] (2019-06_v2.00) - [local copy]
cisBP Danaus_plexippus - [3886 motifs] (2019-06_v2.00) - [local copy]
cisBP Daphnia_pulex - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Dendroctonus_ponderosae - [3846 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_ananassae - [4154 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_erecta - [4347 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_grimshawi - [4226 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_melanogaster - [4514 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_mojavensis - [4293 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_persimilis - [4161 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_pseudoobscura - [4286 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_sechellia - [4352 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_simulans - [4023 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_virilis - [4276 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_willistoni - [4319 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_yakuba - [4326 motifs] (2019-06_v2.00) - [local copy]
cisBP Heliconius_melpomene - [3647 motifs] (2019-06_v2.00) - [local copy]
cisBP Helobdella_robusta - [3660 motifs] (2019-06_v2.00) - [local copy]
cisBP Ixodes_scapularis - [3701 motifs] (2019-06_v2.00) - [local copy]
cisBP Lottia_gigantea - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Lucilia_cuprina - [3942 motifs] (2019-06_v2.00) - [local copy]
cisBP Megaselia_scalaris - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Melitaea_cinxia - [3363 motifs] (2019-06_v2.00) - [local copy]
cisBP Nasonia_vitripennis - [4064 motifs] (2019-06_v2.00) - [local copy]
cisBP Nematostella_vectensis - [3571 motifs] (2019-06_v2.00) - [local copy]
cisBP Octopus_bimaculoides - [3795 motifs] (2019-06_v2.00) - [local copy]
cisBP Onchocerca_volvulus - [2988 motifs] (2019-06_v2.00) - [local copy]
cisBP Pediculus_humanus - [4057 motifs] (2019-06_v2.00) - [local copy]
cisBP Pristionchus_pacificus - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Rhodnius_prolixus - [3380 motifs] (2019-06_v2.00) - [local copy]
cisBP Schistosoma_mansoni - [3181 motifs] (2019-06_v2.00) - [local copy]
cisBP Solenopsis_invicta - [3658 motifs] (2019-06_v2.00) - [local copy]
cisBP Strigamia_maritima - [3791 motifs] (2019-06_v2.00) - [local copy]
cisBP Strongylocentrotus_purpuratus - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Tetranychus_urticae - [3909 motifs] (2019-06_v2.00) - [local copy]
cisBP Tribolium_castaneum - [4101 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichinella_spiralis - [3131 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichoplax_adhaerens - [2901 motifs] (2019-06_v2.00) - [local copy]
cisBP Zootermopsis_nevadensis - [3945 motifs] (2019-06_v2.00) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7086 motifs] (2019-07) - [local copy]
JASPAR core nonredundant insects - [133 motifs] (2018) - [local copy]
JASPAR core nonredundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core nonredundant urochordates - [1 motifs] (2018) - [local copy]
JASPAR core redundant insects - [140 motifs] (2018) - [local copy]
JASPAR core redundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core redundant urochordates - [1 motifs] (2018) - [local copy]

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]
cisBP Aegilops_tauschii - [1177 motifs] (2019-06_v2.00) - [local copy]
cisBP Amborella_trichopoda - [1291 motifs] (2019-06_v2.00) - [local copy]
cisBP Arabidopsis_lyrata - [1556 motifs] (2019-06_v2.00) - [local copy]
cisBP Brachypodium_distachyon - [1295 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_napus - [25 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_oleracea - [1539 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_rapa - [1532 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlamydomonas_reinhardtii - [340 motifs] (2019-06_v2.00) - [local copy]
cisBP Cucumis_sativus - [1398 motifs] (2019-06_v2.00) - [local copy]
cisBP Fragaria_vesca - [1363 motifs] (2019-06_v2.00) - [local copy]
cisBP Glycine_max - [1491 motifs] (2019-06_v2.00) - [local copy]
cisBP Gossypium_raimondii - [1448 motifs] (2019-06_v2.00) - [local copy]
cisBP Helianthus_annuus - [4 motifs] (2019-06_v2.00) - [local copy]
cisBP Hordeum_vulgare - [1279 motifs] (2019-06_v2.00) - [local copy]
cisBP Leersia_perrieri - [1300 motifs] (2019-06_v2.00) - [local copy]
cisBP Manihot_esculenta - [1425 motifs] (2019-06_v2.00) - [local copy]
cisBP Medicago_truncatula - [1422 motifs] (2019-06_v2.00) - [local copy]
cisBP Musa_acuminata - [1391 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_barthii - [1296 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_brachyantha - [1264 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glaberrima - [1281 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glumaepatula - [1311 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_indica - [1310 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_longistaminata - [1151 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_meridionalis - [1289 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_nivara - [1297 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_punctata - [1341 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_rufipogon - [1302 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_sativa - [1321 motifs] (2019-06_v2.00) - [local copy]
cisBP Ostreococcus_lucimarinus - [418 motifs] (2019-06_v2.00) - [local copy]
cisBP Phaseolus_vulgaris - [12 motifs] (2019-06_v2.00) - [local copy]
cisBP Physcomitrella_patens - [1033 motifs] (2019-06_v2.00) - [local copy]
cisBP Populus_trichocarpa - [1428 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_mume - [1386 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_persica - [1406 motifs] (2019-06_v2.00) - [local copy]
cisBP Selaginella_moellendorffii - [1077 motifs] (2019-06_v2.00) - [local copy]
cisBP Setaria_italica - [1305 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_lycopersicum - [1399 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_tuberosum - [1361 motifs] (2019-06_v2.00) - [local copy]
cisBP Sorghum_bicolor - [1306 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_aestivum - [1293 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_urartu - [1124 motifs] (2019-06_v2.00) - [local copy]
cisBP Vitis_vinifera - [1418 motifs] (2019-06_v2.00) - [local copy]
cisBP Zea_mays - [1334 motifs] (2019-06_v2.00) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1745 motifs] (2019-07) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]
JASPAR core redundant plants - [501 motifs] (2018) - [local copy]

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918) - [local copy]
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
cisBP Saccharomyces_cerevisiae - [1288 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant fungi - [176 motifs] (2018) - [local copy]
JASPAR core redundant fungi - [177 motifs] (2018) - [local copy]

Prokaryotes

DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11) - [local copy]
RegulonDB prokaryotes - [93 motifs] (2015_08) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11145 motifs] (2019-07) - [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

 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

      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