This program was designed to simplify the task of adjusting a gene's codon usage to the preferred codon usage of a specific target organism. In some organisms or organelles, the codon usage is extremely biased and it has been shown that protein expression yield can strongly depend on the codon usage of a gene. The production efficiency of biotechnologically relevant proteins in these systems can be significantly increased by optimizing the codon usage.

    In addition to simply rewriting the gene's DNA sequence to match your favourite organisms preferred codon usage, CodonWorkbench provides some basic tools to estimate the deviation of codon usage from the desired one, or directly compare the codon usage tables of source and target organisms.

Features

• A standard set of codon usage tables is packaged with the program. If you need another organism you can download anything that has been deposited in the Kazusa Codon Usage Database (http://www.kazusa.or.jp/codon/)

• Or create your own table from scratch or based on a downloaded table.

• Compare the codon usage of 2 different organisms.

• Estimate the deviation of your gene of choice from the optimal codon usage of the desired target organism.

• Automatically scan for repetetive regions in the optimized sequence.

• Evaluation of statistical sequence parameters (complexity, GC content, composition).

• Most common nucleotide (GenBank, FASTA) and protein sequence file formats (GenPept, FASTA) are supported for input and output.

• Nice  rich text file (RTF) output of most text display windows supported.

• Different optimization strategies - see the 'General' section of the program settings for a description.

• Fewer bugs ...

• Please note that the program is still under development (as the version number indicates) and there are some features which might not work correctly (or at all). The features listed above, though, are already functional.

Download

    The program requires Java version 6.0 (1.6) to run. If an appropriate Java runtime environment is not already installed on your system, you can obtain it here.

    Installer packages for Linux and Windows are available - the program also runs on Mac OS X (you should use the Linux installer package. In addition you'll have to download and install Apple's Java 6 runtime).