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
Record's date: 2025-02-24
Paper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-3-38
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Paper 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
Article's DOI: 10.1186/1745-6150-3-38
Entity: Universitat Rovira i Virgili
Journal publication year: 2008
Publication Type: Journal Publications
Repositori URV