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

Identifier:  imarina:6385488

Handle: https://hdl.handle.net/20.500.11797/imarina6385488

Authors:  Puigbo, Pere; Guzman, Eduard; Romeu, Antoni; Garcia-Vallve, Santiago

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 precomputed 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. © 2007 The Author(s).