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 collection in list (a box will appear to select each matrix individually)

View matrix descriptions

Vertebrates

Hocomoco (Human TFs) - [771 motifs] (2017-10)
Hocomoco (Mouse TFs) - [531 motifs] (2017-10)
Homer (Human TF motifs) - [332 motifs] (2016-07)
Jolma_2013 (Human TFs) - [818 motifs] (2015-11)
Jolma_2013 (Human TFs dimers) - [664 motifs] (2016-05)
RSAT non-redundant vertebrates - [2233 motifs] (2017)
cisBP human - [1832 motifs] (2014-10_v0.9)
cisBP mouse - [1715 motifs] (2014-10_v0.9)
Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06)
hPDI (Human TFs identified by protein microarray assays) - [437 motifs] (2016-06)
JASPAR core nonredundant vertebrates - [579 motifs] (2018)

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11)
DrosophilaTFs - [61 motifs] (2015-11)
Drosophila IDMMPMM - [39 motifs] (2010_11)
RSAT non-redundant insects - [350 motifs] (2017)
cisBP c_elegans - [1499 motifs] (2015-05_v1.02)
cisBP drosophila - [1427 motifs] (2014-10_v0.9)
footprintDB-metazoa [only metazoa DNA motifs] - [7122 motifs] (2017-09)
JASPAR core nonredundant insects - [133 motifs] (2018)
JASPAR core nonredundant nematodes - [26 motifs] (2018)
JASPAR core nonredundant urochordates - [1 motifs] (2018)

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11)
Athamap (A thaliana) - [84 motifs] (2015-11)
RSAT non-redundant plants - [306 motifs] (2017)
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06)
footprintDB-plants [only plant DNA motifs] - [1784 motifs] (2017-09)
JASPAR core nonredundant plants - [489 motifs] (2018)

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918)
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02)
JASPAR core nonredundant fungi - [176 motifs] (2018)

Prokaryotes

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

Multi-organisms

footprintDB all - [11296 motifs] (2017-09)
JASPAR core nonredundant all - [1404 motifs] (2018)


Or select a file to upload


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  not seeing your favorite organism in the list ? Contact us to have it installed
      Sequence type  
    Upload your own background file     
        Format 

Pseudo-frequencies

Output 

      MANUAL