BRACIL-IA

This code genome accessibility for transcription factor (TF)-binding in Bacteria.

Transcription factors need physical access to DNA it can potentially bind. However, prior to this work it was impossible to measure and assess DNA accessibility in bacteria.

This code uses ChIP-seq from multiple experiments to infer the hidden variable for genome accessibility. This is performed by a linear mixed effect model that considers two parameters: DNA affinity and DNA accessibility.

The fundaments for this code and its biological relevance is described in the following reference:
Gomes ALC, Wang HH (2016) The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. PLoS Comput Biol 12(4): e1004891. doi:10.1371/journal.pcbi.1004891