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


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