Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels.
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.
A translation rate calculator. Users can apply this software tool in two different ways. First, UTR Designer can be used to predict the expression level of a particular mRNA sequence when given the 5′-UTR and target coding sequence (reverse engineering). Second, UTR Designer can be used to generate 5′-UTR sequences and optimize coding sequences (within the same codon preference) to meet a specific target expression level (forward engineering).
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.
A predictive combinatorial design method which systematically searches a large combinatorial space of expression levels. UTR Library Designer accomplishes this by designing synthetic translation initiation region of mRNAs in a predictive way based on a thermodynamic model and genetic algorithm.
Provides a platform gathering ten sequence analysis. SeqCalc is divided into three sections: (i) "nucleotide calc" permits to compute codon statistics, annealing temperature or sequence, and includes some convertors and an ORF finder; (ii) "protein calc" authorizes to calculate iso-electric point and protein properties as well as to extract protein secondary structures and ;(iii) the "common calc" runs analysis on both protein and nucleotide sequences.
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.
A web app for the computational design of conformation-based riboregulation. RiboMaker reads the sequence and structure specifications, which codify for a gene regulatory behaviour, and optimizes the sequences of a small regulatory RNA and a 5'-untranslated region for an efficient intermolecular interaction. To this end, it implements an evolutionary design strategy, where random mutations are selected according to a physicochemical model based on free energies.