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

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.

Figure 1.

Outputs provided from the optimization of a DNA sequence: (a) the optimized and query sequences and the indices (CAI, ENc and%G + C) for evaluating the optimization process, (b) codon usage tables of the query and optimized sequences, (c) query and optimized sequence alignment to show changes in nucleotides (transitions or transversions) and (d) graphical view of the codon weight chart.