This page contains a list of computational methods and resources that we have developed. Please do not hessitate to contact us if you have any problems or questions.

ProBound - A software that analyzes sequencing data from randomized binding assays in order to learn energetic models of sequence recognition. Please visit the dedicated website to use ProBound or read the paper for additional information.
MotifCentral - This is an online database containing curated binding models for hundreds of transcription models (learned using ProBound, see above). Please visit motifcentral.org or read the paper for additional information.
Shapalizer - This method analyzes transcription factor binding models (generated by, for example, ProBound or NRLB) in order to identify statistically robust instances of ‘ DNA shape’ recognition. Please visit GitHub to use the method or read the paper for additional information.