Nucleic Acids Research Advance Access published online on April 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm219
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OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
1Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel·li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain and 2Institut Català de la Salut, Àrea Bàsica de Salut, Tarragona 2, Spain
*To whom correspondence should be addressed. Tel: +34 977558778; Fax: +34 977558232; Email: santi.garcia-vallve{at}urv.net
Received January 29, 2007. Revised March 22, 2007. Accepted March 28, 2007.
OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the ‘one amino acid–one codon’ method, a guided random method based on a Monte Carlo algorithm, and a new method 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 pre-computed codon usage tables from a predicted group of highly expressed genes from more than 150 prokaryotic species under strong translational selection. These groups of highly expressed genes have been predicted using a new iterative algorithm. In addition, users can use, as a reference set, a pre-computed table containing the mean codon usage of ribosomal protein genes and, as a novelty, the tRNA gene-copy numbers. OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER.
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