ModCRElib: a standalone package to model cis-regulatory elements

The ModCRElib package provides various tools for the analysis and modelling of transcription factor (TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF-binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF-binding sites, and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide five example uses of ModCRElib. This includes (i) TF-binding affinity prediction, (ii) TF ensemble pattern of bindings (aggregation of motifs), (iii) characterization of specificity in TF-binding sites along target DNA sequences, (iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA.