Examining DNA Breathing with pyDNA-EPBD.
Anowarul KabirManish BhattaraiKim Ø RasmussenAmarda ShehuAnny UshevaAlan R BishopBoian S AlexandrovPublished in: bioRxiv : the preprint server for biology (2023)
We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability,DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.