JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.


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JCat was published in NAR (Nucleic Acids Research).

Introduction

The CodonAdaptationTool (JCAT) presents a simple method to adapt the Codon Usage to most sequenced prokaryotic organisms and selected eukaryotic organisms. The codon adaptation plays a major role in cases where foreign genes are expressed in hosts and the codon usage of the host differs from that of the organism where the gene stems from. Unadapted codons in the host can for example lead to a minor expression rate.
The adaptation is based on CAI-values proposed by PM Sharp et.al. The CAI-values were calculated by applying an algorithm from A Carbone et. al. The eukaryotic genomes of mouse and human contain different kinds of biases along the chromosomes and the algorithm is not perfectly suited for this problem. Results in this field should be handled with care. The mean codon usage for a certain organism was derrived by summing over all CAI-values of all genes of this organism (except genes without an amino acid sequence, e.g. RNAs) devided by the number of genes. This data is also presented in the graphical output of the codon adaptation.
As a further option for the codon adaptation the opportunity to avoid rho-independent trancription terminators is provided. The algorithm for the prediction of these structures is based on a model from MD Ermolaeva et. al. For more details see the literature section.
Another feature is the possibility to avoid restriction enzyme binding sites in the adapted DNA. The data for the restriction enzymes was therefor derrived from the "The Restriction Enzyme Database" (REBASE).