RSAT - matrix-scan QUICK and SIMPLE

Scan a DNA sequence with a profile matrix
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

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Sequences Sequence       Format Paste your sequence in the box below

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Mask 

Matrix Matrix (or matrices)        Format 

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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 - [0 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 - [0 motifs] (2019-06_v2.00) - [local copy]
cisBP Brugia_malayi - [0 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]

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]

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  
      MANUAL MAIL