{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T19:46:54Z","timestamp":1779306414822,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases.<\/jats:p>\n               <jats:p>Availability: Availability through the P\u00f4le Bioinformatique Lyonnais (PBIL) Web server at http:\/\/pbil.univ-lyon1.fr\/datasets\/charif04\/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.<\/jats:p>\n               <jats:p>Contact: \u00a0http:\/\/pbil.univ-lyon1.fr\/members\/lobry<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti037","type":"journal-article","created":{"date-parts":[[2004,9,17]],"date-time":"2004-09-17T00:13:37Z","timestamp":1095380017000},"page":"545-547","source":"Crossref","is-referenced-by-count":109,"title":["Online synonymous codon usage analyses with the ade4 and seqinR packages"],"prefix":"10.1093","volume":"21","author":[{"given":"D.","family":"Charif","sequence":"first","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive\u2014CNRS UMR 5558, and INRIA Helix project, Universit\u00e9 Claude Bernard\u2014Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Thioulouse","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive\u2014CNRS UMR 5558, and INRIA Helix project, Universit\u00e9 Claude Bernard\u2014Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. R.","family":"Lobry","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive\u2014CNRS UMR 5558, and INRIA Helix project, Universit\u00e9 Claude Bernard\u2014Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G.","family":"Perri\u00e8re","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive\u2014CNRS UMR 5558, and INRIA Helix project, Universit\u00e9 Claude Bernard\u2014Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,9,16]]},"reference":[{"key":"2023013107235211600_B1","unstructured":"Benz\u00e9cri, J.-P. 1983Analyse de l\u2019inertie intra-classe par l\u2019analyse d\u2019un tableau des correspondances. Les Cahiers de l'Analyse des Donn\u00e9es8351\u2013358"},{"key":"2023013107235211600_B2","doi-asserted-by":"crossref","unstructured":"Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G. 1985ACNUC\u2014a portable system for nucleic acid sequence databases: logical and physical designs and usage. Comput. Applic. Biosci.1167\u2013172","DOI":"10.1093\/bioinformatics\/1.3.167"},{"key":"2023013107235211600_B3","unstructured":"Ihaka, R. and Gentleman, R. 1996R: A language for data analysis and graphics. J. Comp. Graph. Stat.5299\u2013314"},{"key":"2023013107235211600_B4","unstructured":"Lobry, J.R. and Chessel, D. 2003Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J. Appl. Genet.44235\u2013261"},{"key":"2023013107235211600_B5","unstructured":"McInerney, J.O. 1998GCUA (General Codon Usage Analysis). Bioinformatics14372\u2013373"},{"key":"2023013107235211600_B6","unstructured":"Perri\u00e8re, G. and Thioulouse, J. 2002Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res.304548\u20134555"},{"key":"2023013107235211600_B7","doi-asserted-by":"crossref","unstructured":"Sharp, P.M., Tuohy, T.M.F., Mosurski, K.R. 1986Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res.145125\u20135143","DOI":"10.1093\/nar\/14.13.5125"},{"key":"2023013107235211600_B8","unstructured":"Thioulouse, J., Chessel, D., Dol\u00e9dec, S., Olivier, J.M. 1997ADE-4: a multivariate analysis and graphical display software. Stat. Comput.775\u201383"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/4\/545\/48965146\/bioinformatics_21_4_545.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/4\/545\/48965146\/bioinformatics_21_4_545.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T09:55:41Z","timestamp":1675158941000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/4\/545\/203393"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,9,16]]},"references-count":8,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2005,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti037","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,2,15]]},"published":{"date-parts":[[2004,9,16]]}}}