Optimizing the codon usage of a DNA sequence with OPTIMIZER

Optimizer: A web server utility that optimize
a DNA or Protein sequence.

Created by P.Puigbo (July 2005)
(Last update April 2007)
Evolutionary Genomics Group. Biochemistry and Biotechnology Department
Universitat Rovira i Virgili (URV). Tarragona. Spain.

OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Users can introduce their own preference tables to be used in the optimization process or use pre-computed tables from more than 150 prokaryotic species under a strong translational selection. Three methods of optimization are available: the 'one amino acid - one codon' approach, a random approach or an intermediate one. Several options, such as avoiding specific restriction sites and several outputs, are also available. This server can be useful for predicting and optimizing the level expression of a gene in heterologous gene expression. See an example of a DNA sequence from Bacteroides thetaiotaomicron. See an example of a Protein sequence from Bacteroides thetaiotaomicron

How to cite:
- Puigbo P., Guzmen E.Romeu A. and Garcia-Vallve S. 2007 OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research, 35:W126-W131.

- Puigbo P., Romeu A. and Garcia-Vallve S. 2008. HEG-DB: a datase of predict highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Research. 36:D524-7.

Step 1) Paste your sequence in the text box and then choose the type of pasted sequence (DNA or Protein) and click on 'CONTINUE >' button.

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