RSA-tools - 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 

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

K fold validation 

Only the first matrix will be taken in acount

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 

    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 

    Tag for this data set

3 - Background

Background model estimation method

Pseudo-frequencies

Output