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).
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].