title: OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.
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.
authors: Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), Tarragona, Spain.
authors: Pere
authors: P
authors: Puigbò
authors: Eduard
authors: E
authors: Guzmán
authors: Antoni
authors: A
authors: Romeu
authors: Santiago
authors: S
authors: Garcia-Vallvé
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D004247:DNA; D015870:Gene Expression; D005786:Gene Expression Regulation; D020407:Internet; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D012270:Ribosomes / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003062:Codon; D004247:DNA