I wish to introduce the OPTIMIZER web-server that optimizes the codon usage of a gene to increase its expression level. This web-server is focused on the heterologous, or even homologous, gene expression in bacterial hosts. Two indices, CAI and ENc (effective number of codons), are used to measure the optimization process.
Three methods of optimization are available:
- The 'one amino acid - one codon' method.
- A guided random method based on a Monte Carlo algorithm.
-The ‘customized one amino acid - one codon’ designed to maximize the optimization with the fewest changes in the query sequence.
One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using the following pre-computed tables from more than 150 prokaryotic species under strong translational selection:
- Codon usage from a Predicted Group of Highly Expressed Genes.
- Codon usage from the Group of Ribosomal Protein Genes.
- tRNA Gene Copy Numbers (tGCN).
Additionally, codon usage tables from the Codon Usage database (CUTG) can also be used.
OPTIMIZER is accessible free of charge at
http://genomes.urv.es/OPTIMIZER .
For more details see the article Puigbo et al. 2007 Nucleic Acids Research, doi:10.1093/nar/gkm219 .
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Pere Puigbò Avalos, PhD Student
Evolutionary Genomics Group,
Biochemistry and Biotechnology Department,
Rovira i Virgily University.
C/Marcel·lí domingo s/n. 43007. Campus Sescelades. Tarragona.
Phone: 0034.977.55.84.86
Web Page:
http://genomes.urv.catE-mail:
ppuigbo@...
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