ArticleNucleic acids research2007
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 275 papers.
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Who cites it
275 citing papers in PubMed.
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- N-Terminal Actin-Binding Site of Lmod2 Promotes Controlled Pointed End Elongation.Circulation research · 2026Article
- Pichia-CLM: A language model-based codon optimization pipeline forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Development of a novel multi-epitope vaccine against Ureaplasma urealyticum infection through reverse vaccinology approach.Molecular diversity · 2026Article
- Expression of Recombinant Phytoplasma Proteins in E. coli.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Overcoming the Challenges of Producing Plant Phytochromes in Escherichia coli.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Sustainable production of myoglobin meat protein in plant chloroplasts.Frontiers in plant science · 2026Article
- Design of a novel multi epitope antigen for diagnosis of visceral leishmaniasis using an immunoinformatics approach.Scientific reports · 2025Article
- Validated antimalarial drug target discovery using genome-scale metabolic modeling.Antimicrobial agents and chemotherapy · 2025Article
- A CRISPRi Gene Regulation System for Bifidobacteria.Microbial biotechnology · 2025Article
- Computational design of an mRNA vaccine targeting antifungal-resistant Lomentospora prolificans.Scientific reports · 2025Article
- Heterologous DNA-Adenovirus Prime-Boost Strategy Expressing Bluetongue Virus VP2 and VP7 Proteins Protects Against Virulent Challenge.Vaccines · 2025Article
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- Codon Optimization is Required to Express Fluorogenic Reporter Proteins in Lactococcus lactis.Molecular biotechnology · 2025Article
- Article
215 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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