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

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W126-31. doi: 10.1093/nar/gkm219. Epub 2007 Apr 16.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Base Sequence
  • Codon / genetics*
  • Computational Biology / methods*
  • DNA*
  • Gene Expression
  • Gene Expression Regulation
  • Internet
  • Molecular Sequence Data
  • Protein Biosynthesis
  • Ribosomes / genetics
  • Sequence Analysis, DNA
  • Software*


  • Codon
  • DNA