The regshape R package provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.
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Bioinformatics. 2015 Jun 30. pii: btv391
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J, Ramsey SA.