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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W126-31. Epub 2007 Apr 16.

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

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1
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), Tarragona, Spain.

Abstract

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.

PMID:
17439967
PMCID:
PMC1933141
DOI:
10.1093/nar/gkm219
[Indexed for MEDLINE]
Free PMC Article
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