Author, as appears in the article.: Puigbo, Pere; Bravo, Ignacio G.; Garcia-Vallve, Santiago;
Department: Bioquímica i Biotecnologia
URV's Author/s: Garcia Vallve, Santiago / PUIGBÒ AVALOS, PEDRO
Keywords: Server Prokaryotic complete genomes Papillomavirus genomes Metabolism Index Highly expressed genes Db Database Cycle Bias
Abstract: The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set.We describe here CAIcal, a web-server available at http://genomes.urv.es/CAIcal that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a stand alone application for local use.The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.
Thematic Areas: Modeling and simulation Medicina ii Medicina i Matemática / probabilidade e estatística Immunology General biochemistry,genetics and molecular biology General agricultural and biological sciences Ecology, evolution, behavior and systematics Ciências biológicas ii Ciências biológicas i Ciência da computação Biotecnología Biology Biodiversidade Biochemistry, genetics and molecular biology (miscellaneous) Biochemistry, genetics and molecular biology (all) Astronomia / física Applied mathematics Agricultural and biological sciences (miscellaneous) Agricultural and biological sciences (all)
licence for use: https://creativecommons.org/licenses/by/3.0/es/
ISSN: 17456150
Author's mail: santi.garcia-vallve@urv.cat
Author identifier: 0000-0002-0348-7497
Record's date: 2023-02-18
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-3-38
Papper original source: Biology Direct. 3 (38): 38-
APA: Puigbo, Pere; Bravo, Ignacio G.; Garcia-Vallve, Santiago; (2008). CAIcal: A combined set of tools to assess codon usage adaptation. Biology Direct, 3(38), 38-. DOI: 10.1186/1745-6150-3-38
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Article's DOI: 10.1186/1745-6150-3-38
Entity: Universitat Rovira i Virgili
Journal publication year: 2008
Publication Type: Journal Publications
Repositori URV