Pinetree: a step-wise gene expression simulator with codon-specific translation rates

Abstract

Motivation: Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility.

Results: We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes.

Availability and implementation: Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).