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RBS Calculator / Ribosome Binding Site Calculator
Controls translation initiation and protein expression in bacteria. RBS Calculator is a predictive design method that: (i) predicts the rate of translation initiation for every start codon in an mRNA transcript in its reverse engineering mode, and (ii) optimizes a synthetic RBS sequence to achieve a targeted translation initiation rate in its forward engineering mode. This method employs a thermodynamic model of bacterial translation initiation to calculate the Gibbs free energy of ribosome binding.
Predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The synthetic RBS could be used to maximize translation efficiency for the intensive production of therapeutics or industrial proteins. It may assist in balancing the levels of enzymes in a synthetic metabolic pathway to optimize the metabolic flux, or it could be used to optimize protein expression of components in constructed genetic circuits to ensure robust operation.
AnaCoDa / Analyzing Codon Data
Allows analysis of genome-scale data like coding sequences and ribosome footprinting data using evolutionary or analytical models in a Bayesian framework. AnaCoDa is an R package developed for analyzing selection on synonymous codon usage in the form of ribosome overhead cost. The software provides four models to analyze codon counts obtained from coding sequences or ribosome foot-printing experiments, as well as a mixture distribution option to all implemented models.
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