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Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences

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datacite.rightshttp://purl.org/coar/access_right/c_abf2
dc.creatorMarrero-Ponce, Y.
dc.creatorMarrero-Ponce, Y.
dc.creatorTellez-Ibarra, R.
dc.creatorLlorente-Quesada, M.T.
dc.creatorSalgado, J.
dc.creatorBarigye, S.J.
dc.creatorLiu, J.
dc.date.accessioned2019-11-06T19:05:19Z
dc.date.available2019-11-06T19:05:19Z
dc.date.issued2015
dc.description.abstractMotivation: 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 nonredundant sequence database. For this purpose, a new software tool is introduced. 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 16 990 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. © The Author 2015. Published by Oxford University Press. All rights reserved.eng
dc.description.notesAntimicrobial Cationic Peptides
dc.format.mediumRecurso electrónico
dc.format.mimetypeapplication/pdf
dc.identifier.citationBioinformatics; Vol. 31, Núm. 15; pp. 2553-2559
dc.identifier.doi10.1093/bioinformatics/btv180
dc.identifier.instnameUniversidad Tecnológica de Bolívar
dc.identifier.issn1367-4803
dc.identifier.reponameRepositorio UTB
dc.identifier.urihttps://hdl.handle.net/20.500.12585/8759
dc.language.isoeng
dc.publisherOxford University Press
dc.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.rights.ccAtribución-NoComercial 4.0 Internacional
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.sourcehttps://www2.scopus.com/inward/record.uri?eid=2-s2.0-84943601205&doi=10.1093%2fbioinformatics%2fbtv180&partnerID=40&md5=141f38519649235606ce49338df9709e
dc.sourceScopus 56035076700
dc.sourceScopus 55665599200
dc.sourceScopus 56897175400
dc.sourceScopus 56035437800
dc.sourceScopus 7102811634
dc.sourceScopus 55363486500
dc.sourceScopus 56896521800
dc.subject.keywordsAntimicrobial cationic peptide
dc.subject.keywordsAlgorithm
dc.subject.keywordsChemistry
dc.subject.keywordsHuman
dc.subject.keywordsNucleic acid database
dc.subject.keywordsProcedures
dc.subject.keywordsProtein database
dc.subject.keywordsSequence analysis
dc.subject.keywordsSoftware
dc.subject.keywordsAlgorithms
dc.subject.keywordsAntimicrobial cationic peptides
dc.subject.keywordsDatabases, Nucleic Acid
dc.subject.keywordsDatabases, Protein
dc.subject.keywordsHumans
dc.subject.keywordsSequence Analysis, Protein
dc.subject.keywordsSoftware
dc.titleOverlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
dc.type.driverinfo:eu-repo/semantics/article
dc.type.hasversioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículo
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oaire.resourceTypehttp://purl.org/coar/resource_type/c_6501
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85

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Universidad Tecnológica de Bolívar - 2017 Institución de Educación Superior sujeta a inspección y vigilancia por el Ministerio de Educación Nacional. Resolución No 961 del 26 de octubre de 1970 a través de la cual la Gobernación de Bolívar otorga la Personería Jurídica a la Universidad Tecnológica de Bolívar.