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Examining DNA Breathing with pyDNA-EPBD.

Anowarul KabirManish BhattaraiKim Ø RasmussenAmarda ShehuAnny UshevaAlan R BishopBoian S Alexandrov
Published 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.
Keyphrases
  • circulating tumor
  • cell free
  • single molecule
  • monte carlo
  • nucleic acid
  • primary care
  • healthcare
  • circulating tumor cells
  • quality improvement
  • dna methylation