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bioRxiv · 10.1101/339994

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

Jack, B. R.·Wilke, C. O.
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Abstract

MotivationStochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programming interfaces, which limits their utility.\n\nResultsWe 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.\n\nAvailabilityPinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).

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Jack, B. R., Wilke, C. O.. 2018-06-07. Pinetree: a step-wise gene expression simulator with codon-specific translation rates. https://doi.org/10.1101/339994

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