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OPTIMIZER: a web server for optimizing the codon usage of DNA sequences

2007; Oxford University Press; Volume: 35; Issue: Web Server Linguagem: Inglês

10.1093/nar/gkm219

1362-4962

Pere Puigbò, Efrain Guzman, A. Romeu, Santiago Garcı́a-Vallvé,

RNA modifications and cancer

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.