{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,14]],"date-time":"2025-04-14T20:34:43Z","timestamp":1744662883622},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Numerous software applications exist to deal with synthetic gene design, granting the field of heterologous expression a significant support. However, their dispersion requires the access to different tools and online services in order to complete one single project. Analyzing codon usage, calculating codon adaptation index (CAI), aligning orthologs and optimizing genes are just a few examples. A software application, EuGene, was developed for the optimization of multiple gene synthetic design algorithms. In a seamless automatic form, EuGene calculates or retrieves genome data on codon usage (relative synonymous codon usage and CAI), codon context (CPS and codon pair bias), GC content, hidden stop codons, repetitions, deleterious sites, protein primary, secondary and tertiary structures, gene orthologs, species housekeeping genes, performs alignments and identifies genes and genomes. The main function of EuGene is analyzing and redesigning gene sequences using multi-objective optimization techniques that maximize the coding features of the resulting sequence.<\/jats:p>\n Availability: EuGene is freely available for non-commercial use, at http:\/\/bioinformatics.ua.pt\/eugene<\/jats:p>\n Contact: \u00a0paulogaspar@ua.pt<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts465","type":"journal-article","created":{"date-parts":[[2012,7,31]],"date-time":"2012-07-31T06:55:55Z","timestamp":1343717755000},"page":"2683-2684","source":"Crossref","is-referenced-by-count":59,"title":["EuGene: maximizing synthetic gene design for heterologous expression"],"prefix":"10.1093","volume":"28","author":[{"given":"Paulo","family":"Gaspar","sequence":"first","affiliation":[{"name":"1 DETI\/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal and 2Department of Biology and CESAM, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal"}]},{"given":"Jos\u00e9 Lu\u00eds","family":"Oliveira","sequence":"additional","affiliation":[{"name":"1 DETI\/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal and 2Department of Biology and CESAM, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal"}]},{"given":"J\u00f6rg","family":"Frommlet","sequence":"additional","affiliation":[{"name":"1 DETI\/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal and 2Department of Biology and CESAM, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal"}]},{"given":"Manuel A.S.","family":"Santos","sequence":"additional","affiliation":[{"name":"1 DETI\/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal and 2Department of Biology and CESAM, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal"}]},{"given":"Gabriela","family":"Moura","sequence":"additional","affiliation":[{"name":"1 DETI\/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal and 2Department of Biology and CESAM, University of Aveiro, Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2012,7,30]]},"reference":[{"key":"2023012513140390900_bts465-B1","doi-asserted-by":"crossref","first-page":"e2189","DOI":"10.1371\/journal.pone.0002189","article-title":"Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host","volume":"3","author":"Angov","year":"2008","journal-title":"PLoS One"},{"key":"2023012513140390900_bts465-B2","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1101\/gad.207701","article-title":"Translational misreading: a tRNA modification counteracts a+ 2 ribosomal frameshift","volume":"15","author":"Br\u00e9geon","year":"2001","journal-title":"Genes Develop."},{"key":"2023012513140390900_bts465-B3","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"Muscle: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012513140390900_bts465-B4","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1111\/j.1365-2958.2006.05110.x","article-title":"Influences on gene expression in vivo by a Shine\u2013Dalgarno sequence","volume":"60","author":"Jin","year":"2006","journal-title":"Mol. 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