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In the context of the study of the proximal origins of SARS-CoV-2 coronavirus, we wanted to construct an alignment of genomes closely related to SARS-CoV-2 using both coding and non-coding sequences. To our knowledge, there is no tool that can be used to construct this type of alignment, which motivated the creation of CNCA.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>CNCA is a web tool that aligns annotated genomes from GenBank files. It generates a nucleotide alignment that is then updated based on the protein sequence alignment. The output final nucleotide alignment matches the protein alignment and guarantees no frameshift. CNCA was designed to align closely related small genome sequences up to 50\u00a0kb (typically viruses) for which the gene order is conserved.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>CNCA constructs multiple alignments of small genomes by integrating both coding and non-coding sequences. This preserves regions traditionally ignored in conventional back-translation methods, such as non-coding regions.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05700-1","type":"journal-article","created":{"date-parts":[[2024,2,29]],"date-time":"2024-02-29T18:07:32Z","timestamp":1709230052000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["CNCA aligns small annotated genomes"],"prefix":"10.1186","volume":"25","author":[{"given":"Jean-No\u00ebl","family":"Lorenzi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fran\u00e7ois","family":"Graner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Virginie","family":"Courtier-Orgogozo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillaume","family":"Achaz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,2,29]]},"reference":[{"key":"5700_CR1","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1186\/1471-2105-11-579","volume":"11","author":"A L\u00f6ytynoja","year":"2010","unstructured":"L\u00f6ytynoja A, Goldman N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. 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RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 2003;31:3537\u20139.","journal-title":"Nucleic Acids Res."},{"key":"5700_CR5","doi-asserted-by":"publisher","first-page":"2582","DOI":"10.1093\/molbev\/msy159","volume":"35","author":"V Ranwez","year":"2018","unstructured":"Ranwez V, Douzery EJP, Cambon C, Chantret N, Delsuc F. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol Biol Evol. 2018;35:2582\u20134.","journal-title":"Mol Biol Evol"},{"key":"5700_CR6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0022594","volume":"6","author":"V Ranwez","year":"2011","unstructured":"Ranwez V, Harispe S, Delsuc F, Douzery EJP. MACSE: multiple alignment of coding sequences accounting for frameshifts and stop codons. PLoS ONE. 2011;6: e22594.","journal-title":"PLoS ONE"},{"key":"5700_CR7","doi-asserted-by":"publisher","first-page":"W7","DOI":"10.1093\/nar\/gkq291","volume":"38","author":"F Abascal","year":"2010","unstructured":"Abascal F, Zardoya R, Telford MJ. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 2010;38:W7-13.","journal-title":"Nucleic Acids Res"},{"key":"5700_CR8","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","volume":"17","author":"J Castresana","year":"2000","unstructured":"Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540\u201352.","journal-title":"Mol Biol Evol"},{"key":"5700_CR9","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1186\/s12859-017-1555-6","volume":"18","author":"PL Tzou","year":"2017","unstructured":"Tzou PL, Huang X, Shafer RW. NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. BMC Bioinformatics. 2017;18:138.","journal-title":"BMC Bioinformatics"},{"key":"5700_CR10","doi-asserted-by":"publisher","first-page":"1763","DOI":"10.1093\/bioinformatics\/bty851","volume":"35","author":"PJK Libin","year":"2019","unstructured":"Libin PJK, Deforche K, Abecasis AB, Theys K. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. Bioinformatics. 2019;35:1763\u20135.","journal-title":"Bioinformatics"},{"key":"5700_CR11","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1093\/bioinformatics\/bty121","volume":"34","author":"T Nakamura","year":"2018","unstructured":"Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. 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