STAP (Sequence To Affinity Prediction) predict transcription factor and DNA interaction affinity and the DNA sequence, considering combinatorial interactions of multiple transcription factors. STAP can be applied to analyze ChIP-seq data.
- GNU Scientific Library (GSL).
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PLoS One. 2009 Dec 1;4(12):e8155.
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.