Author, as appears in the article.: Puigbò P; Guzmán E; Romeu A; Garcia-Vallvé S
Department: Bioquímica i Biotecnologia
URV's Author/s: Garcia Vallve, Santiago / GUZMAN DESCARREGA, EDUARDO / PUIGBÒ AVALOS, PEDRO / ROMEU FIGUEROLA, ANTONIO RAMÓN / ROMEU MORENO, ANDRÉS
Keywords: Translation Transfer-rnas Tool Synthetic genes Genomes Expression Escherichia-coli Designer Bias Adaptation index
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 precomputed 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. © 2007 The Author(s).
Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Nutrição Medicina ii Medicina i Matemática / probabilidade e estatística Interdisciplinar Genetics Farmacia Engenharias ii Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências agrárias i Ciência da computação Biotecnología Biodiversidade Biochemistry & molecular biology Astronomia / física
licence for use: https://creativecommons.org/licenses/by/3.0/es/
ISSN: 0305-1048
Author's mail: santi.garcia-vallve@urv.cat
Author identifier: 0000-0002-0348-7497
Last page: W131
Record's date: 2024-10-05
Journal volume: 35
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://academic.oup.com/nar/article/35/suppl_2/W126/2920747
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Papper original source: Nucleic Acids Research. 35 (SUPPL.2): W126-31
APA: Puigbò P; Guzmán E; Romeu A; Garcia-Vallvé S (2007). OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research, 35(SUPPL.2), W126-31. DOI: 10.1093/nar/gkm219
Article's DOI: 10.1093/nar/gkm219
Entity: Universitat Rovira i Virgili
Journal publication year: 2007
First page: W126
Publication Type: Journal Publications
Repositori URV