Affinity prediction algorithm

The affinity prediction algorithm is a custom implementation of a algorithm proposed by Manke et al (2008).

 

It predicts the total affinity to a stretch of DNA (e.g. the promoter region) instead of predicting binding to single sites. The results of this algorithm of all vertebrate transcription factor matrices from Transfac to the promoter sets are stored in a database file.

1) Roider HG, Kanhere A, Manke T, Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics. 2007 Jan 15;23(2):134-41. Epub 2006 Nov 10..