Challenges with Modelling Transcription Factor Binding

Proc. Next Generation Computing Applications (Nextcomp2017), Mauritius, 19-21 July 2008, pp 68-74,

Philip Machanick and Caleb Kipkurui Kibet

Modelling transcription factor binding presents a number of challenges. In its simplest form, binding can be modelled by a consensus sequence but a number of factors including degeneracy of binding sites, alternative modes of bind- ing and differences between artificially-constructed and in vivo DNA make modelling binding complex. In this paper we outline difficulties and report on progress with improving modelling of binding. We focus on improving measurement of binding models, a necessary prerequisite for finding better models.