Describes translation dynamics to the single-nucleotide resolution for entire transcriptome. SMoPT is based on a Markov model of translation using the Gillespie algorithm. It treats the total number of ribosomes, tRNA molecules, and mRNA molecules in the cell as fixed quantities because the dynamics of their production and decay are typically slower than those of protein translation. This tool ignores the details of termination, as well as translation errors.
Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
SMoPT funding source(s)
Supported by the Burroughs Wellcome Fund, the David and Lucile Packard Foundation, the James S. McDonnell Foundation, the Alfred P. Sloan Foundation, the Foundational Questions in Evolutionary Biology Fund (RFP-12-16), the U.S. Army Research Office (grant W911NF-12-1-0552), and grant D12AP00025 from the U.S. Department of the Interior; by The Wellcome Trust grant 077248; and by the Darwin Trust of Edinburgh.