{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T23:57:35Z","timestamp":1783727855182,"version":"3.55.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced.<\/jats:p>\n               <jats:p>Results: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16\u2009990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs.<\/jats:p>\n               <jats:p>Availability and implementation: The regularly updated non-redundant sequence databases and the Dover Analyzer software to perform custom analysis are available at http:\/\/mobiosd-hub.com\/doveranalyzer\/.<\/jats:p>\n               <jats:p>Contact: \u00a0ymarrero77@yahoo.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv180","type":"journal-article","created":{"date-parts":[[2015,3,30]],"date-time":"2015-03-30T00:12:02Z","timestamp":1427674322000},"page":"2553-2559","source":"Crossref","is-referenced-by-count":52,"title":["Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences"],"prefix":"10.1093","volume":"31","author":[{"given":"Longendri","family":"Aguilera-Mendoza","sequence":"first","affiliation":[{"name":"1 Grupo de Investigaci\u00f3n de Bioinform\u00e1tica, Centro de Estudio de Matem\u00e1tica Computacional, Universidad de las Ciencias Inform\u00e1ticas, La Habana, Cuba,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yovani","family":"Marrero-Ponce","sequence":"additional","affiliation":[{"name":"2 Grupo de Investigaci\u00f3n en Estudios Qu\u00edmicos y Biol\u00f3gicos, Facultad de Ciencias B\u00e1sicas, Universidad Tecnol\u00f3gica de Bol\u00edvar, Cartagena de Indias, Bol\u00edvar, Colombia,"},{"name":"3 Facultad de Qu\u00edmica Farmac\u00e9utica, Universidad de Cartagena, Cartagena de Indias, Bol\u00edvar, Colombia,"},{"name":"4 Instituto de Ciencia Molecular (ICMol), Universitat de Val\u00e8ncia, C\/ Catedr\u00e1tico Jos\u00e9 Beltr\u00e1n, 2, 46980, Paterna (Valencia), Spain,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Tellez-Ibarra","sequence":"additional","affiliation":[{"name":"1 Grupo de Investigaci\u00f3n de Bioinform\u00e1tica, Centro de Estudio de Matem\u00e1tica Computacional, Universidad de las Ciencias Inform\u00e1ticas, La Habana, Cuba,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica T.","family":"Llorente-Quesada","sequence":"additional","affiliation":[{"name":"1 Grupo de Investigaci\u00f3n de Bioinform\u00e1tica, Centro de Estudio de Matem\u00e1tica Computacional, Universidad de las Ciencias Inform\u00e1ticas, La Habana, Cuba,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jes\u00fas","family":"Salgado","sequence":"additional","affiliation":[{"name":"4 Instituto de Ciencia Molecular (ICMol), Universitat de Val\u00e8ncia, C\/ Catedr\u00e1tico Jos\u00e9 Beltr\u00e1n, 2, 46980, Paterna (Valencia), Spain,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Barigye","sequence":"additional","affiliation":[{"name":"5 Departamento de Qu\u00edmica, Universidade Federal de Lavras, UFLA Caixa Postal 3037, 37200-000 Lavras, MG, Brazil and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Liu","sequence":"additional","affiliation":[{"name":"6 School of Computing and Mathematics, Faculty of Computing and Engineering, Ulster University, Jordanstown campus, Northern Ireland, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,3,29]]},"reference":[{"key":"2023051308493191100_btv180-B1","doi-asserted-by":"crossref","first-page":"D586","DOI":"10.1093\/nar\/gkh032","article-title":"Antimic: a database of antimicrobial sequences","volume":"32","author":"Brahmachary","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023051308493191100_btv180-B2","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1042\/bst0290565","article-title":") Peptaibols: models for ion channels","volume":"29","author":"Chugh","year":"2001","journal-title":"Biochem. 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