{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T14:13:44Z","timestamp":1764080024645,"version":"3.37.3"},"reference-count":7,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T00:00:00Z","timestamp":1717632000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T00:00:00Z","timestamp":1717632000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"MRC New Investigator Research Grant","award":["MR\/T016019\/1"],"award-info":[{"award-number":["MR\/T016019\/1"]}]},{"DOI":"10.13039\/501100004901","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","doi-asserted-by":"publisher","award":["APQ-01822-18"],"award-info":[{"award-number":["APQ-01822-18"]}],"id":[{"id":"10.13039\/501100004901","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Instituto Nacional de Ci\u00eancia e Tecnologia de Vacina"},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["310531\/2023-3"],"award-info":[{"award-number":["310531\/2023-3"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Gene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication events throughout evolution, resulting in multiple copies of an ancestral gene. Over time, these copies can acquire mutations and structural variations, resulting in members that may vary in size, motif ordering and sequence. Multigene families have been described in a broad range of organisms, from single-celled bacteria to complex multicellular organisms, and have been linked to an array of phenomena, such as host\u2013pathogen interactions, immune evasion and embryonic development. Despite the importance of gene families, few approaches have been developed for estimating and graphically visualizing their diversity patterns and expression profiles in genome-wide studies.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we introduce an R package named dgfr, which estimates and enables the visualization of sequence divergence within gene families, as well as the visualization of secondary data such as gene expression. The package takes as input a multi-fasta file containing the coding sequences (CDS) or amino acid sequences from a multigene family, performs a pairwise alignment among all sequences, and estimates their distance, which is subjected to dimension reduction, optimal cluster determination, and gene assignment to each cluster. The result is a dataset that allows for the visualization of sequence divergence and expression within the gene family, an approximation of the number of clusters present in the family.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p><jats:italic>dgfr<\/jats:italic> provides a way to estimate and study the diversity of gene families, as well as visualize the dispersion and secondary profile of the sequences. The <jats:italic>dgfr<\/jats:italic> package is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/lailaviana\/dgfr\">https:\/\/github.com\/lailaviana\/dgfr<\/jats:ext-link> under the GPL-3 license.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05826-2","type":"journal-article","created":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T10:03:48Z","timestamp":1717668228000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["dgfr: an R package to assess sequence diversity of gene families"],"prefix":"10.1186","volume":"25","author":[{"given":"Laila Viana","family":"Almeida","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jo\u00e3o Lu\u00eds","family":"Reis-Cunha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniella C.","family":"Bartholomeu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,6,6]]},"reference":[{"key":"5826_CR1","doi-asserted-by":"crossref","unstructured":"Ohta T. Gene Families: Multigene Families and Superfamilies. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd; 2008","DOI":"10.1002\/9780470015902.a0005126.pub2"},{"key":"5826_CR2","doi-asserted-by":"publisher","first-page":"2258","DOI":"10.1128\/IAI.06225-11","volume":"80","author":"LM De Pablos","year":"2012","unstructured":"De Pablos LM, Osuna A. Multigene families in Trypanosoma cruzi and their role in infectivity. Infect Immun. 2012;80:2258\u201364.","journal-title":"Infect Immun"},{"key":"5826_CR3","doi-asserted-by":"publisher","first-page":"2397","DOI":"10.1093\/bioinformatics\/btp433","volume":"25","author":"K Bleakley","year":"2009","unstructured":"Bleakley K, Yamanishi Y. Supervised prediction of drug\u2013target interactions using bipartite local models. Bioinformatics. 2009;25:2397\u2013403.","journal-title":"Bioinformatics"},{"key":"5826_CR4","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1590\/S0074-02761909000200008","volume":"1","author":"C Chagas","year":"1909","unstructured":"Chagas C. Nova tripanozomiaze humana: estudos sobre a morfolojia e o ciclo evolutivo do Schizotrypanum cruzi n. gen., n. sp., ajente etiolojico de nova entidade morbida do homem. Mem Inst Oswaldo Cruz. 1909;1:159\u2013218.","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"5826_CR5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009254","volume":"17","author":"W Wang","year":"2021","unstructured":"Wang W, Peng D, Baptista RP, Li Y, Kissinger JC, Tarleton RL. Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease. PLOS Pathog. 2021;17: e1009254.","journal-title":"PLOS Pathog"},{"key":"5826_CR6","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/S0166-6851(01)00245-6","volume":"114","author":"A Acosta-Serrano","year":"2001","unstructured":"Acosta-Serrano A, Almeida IC, Freitas-Junior LH, Yoshida N, Schenkman S. The mucin-like glycoprotein super-family of Trypanosoma cruzi: structure and biological roles. Mol Biochem Parasitol. 2001;114:143\u201350.","journal-title":"Mol Biochem Parasitol"},{"key":"5826_CR7","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/0166-6851(93)90227-O","volume":"59","author":"S Schenkman","year":"1993","unstructured":"Schenkman S, Ferguson MA, Heise N, de Almeida ML, Mortara RA, Yoshida N. Mucin-like glycoproteins linked to the membrane by glycosylphosphatidylinositol anchor are the major acceptors of sialic acid in a reaction catalyzed by trans-sialidase in metacyclic forms of Trypanosoma cruzi. Mol Biochem Parasitol. 1993;59:293\u2013303.","journal-title":"Mol Biochem Parasitol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05826-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-024-05826-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05826-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T10:04:46Z","timestamp":1717668286000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-024-05826-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,6]]},"references-count":7,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["5826"],"URL":"https:\/\/doi.org\/10.1186\/s12859-024-05826-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2024,6,6]]},"assertion":[{"value":"12 January 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 June 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declared no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"207"}}