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Published on: April 26, 2013
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.
Pere Puigbò1, Eduard Guzmán, Antoni Romeu
1Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), Tarragona, Spain.
Nucleic Acids Research
|April 19, 2007
Summary
OPTIMIZER is a web tool that optimizes gene codon usage for higher expression. It offers three methods, including a novel approach for minimal sequence changes, using pre-computed codon usage tables from 150+ prokaryotic species.
Area of Science:
- Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- Gene expression levels are crucial for protein production.
- Codon usage bias significantly impacts translation efficiency.
- Optimizing codon usage can enhance heterologous gene expression.
Purpose of the Study:
- To introduce OPTIMIZER, an online application for optimizing gene codon usage.
- To provide tools for increasing gene expression levels through codon optimization.
- To offer novel methods and reference datasets for codon optimization.
Main Methods:
- Development of an online application (OPTIMIZER) for gene codon optimization.
- Implementation of three optimization strategies: 'one amino acid-one codon', guided random (Monte Carlo), and a novel minimal-change method.
- Utilizing pre-computed codon usage tables from highly expressed genes in over 150 prokaryotic species, predicted via an iterative algorithm.
- Incorporating mean codon usage of ribosomal protein genes and tRNA gene-copy numbers as reference sets.
Main Results:
- OPTIMIZER provides three distinct codon optimization methods.
- The application leverages extensive, curated codon usage data from diverse prokaryotic species.
- A novel optimization method is introduced to minimize sequence alterations while maximizing expression.
- The tool offers pre-computed reference tables, including tRNA gene-copy numbers, for enhanced optimization.
Conclusions:
- OPTIMIZER is a valuable free resource for researchers aiming to enhance gene expression.
- The application facilitates codon optimization using diverse, species-specific datasets.
- The novel optimization method offers a balance between expression enhancement and sequence integrity.
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