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

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.identifier.citationBioinformatics; Vol. 31, Núm. 15; pp. 2553-2559
dc.identifier.issn1367-4803
dc.identifier.urihttps://hdl.handle.net/20.500.12585/8759
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.format.mediumRecurso electrónico
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherOxford University Press
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.titleOverlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
dcterms.bibliographicCitationBrahmachary, M., Antimic: A database of antimicrobial sequences (2004) Nucleic Acids Res., 32, pp. D586-D589
dcterms.bibliographicCitationChugh, J., Wallace, B., Peptaibols: Models for ion channels (2001) Biochem. Soc. Trans., 29, pp. 565-570
dcterms.bibliographicCitationCotter, P.D., Bacteriocins: Developing innate immunity for food (2005) Nat. Rev. Microbiol., 3, pp. 777-788
dcterms.bibliographicCitationDe Jong, A., Bagel2: Mining for bacteriocins in genomic data (2010) Nucleic Acids Res., 38, pp. W647-W651
dcterms.bibliographicCitationEngler, A.C., Emerging trends in macromolecular antimicrobials to fight multi-drug-resistant infections (2012) Nano Today, 7, pp. 201-222
dcterms.bibliographicCitationFjell, C.D., AMPer: A database and an automated discovery tool for antimicrobial peptides (2007) Bioinformatics, 23, pp. 1148-1155
dcterms.bibliographicCitationFjell, C.D., Designing antimicrobial peptides: Form follows function (2012) Nat. Rev. Drug Discov., 11, pp. 37-51
dcterms.bibliographicCitationGanz, T., Defensins: Antimicrobial peptides of innate immunity (2003) Nat. Rev. Immunol., 3, pp. 710-720
dcterms.bibliographicCitationGaspar, D., From antimicrobial to anticancer peptides (2013) A Review. Front. Microbiol., 4, p. 294
dcterms.bibliographicCitationGogoladze, G., DBAASP: Database of antimicrobial activity and structure of peptides (2014) FEMS Microbiol. Lett., 357, pp. 63-68
dcterms.bibliographicCitationGueguen, Y., Penbase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature (2006) Dev. Comp. Immunol., 30, pp. 283-288
dcterms.bibliographicCitationHammami, R., Phytamp: A database dedicated to antimicrobial plant peptides (2009) Nucleic Acids Res., 37, pp. D963-D968
dcterms.bibliographicCitationHammami, R., Bactibase second release: A database and tool platform for bacteriocin characterization (2010) BMC Microbiol., 10, p. 22
dcterms.bibliographicCitationHolland, R.C., Biojava: An open-source framework for bioinformatics (2008) Bioinformatics, 24, pp. 2096-2097
dcterms.bibliographicCitationHolm, L., Sander, C., Removing near-neighbour redundancy from large protein sequence collections (1998) Bioinformatics, 14, pp. 423-429
dcterms.bibliographicCitationJenssen, H., A wide range of medium-sized, highly cationic, a-helical peptides show antiviral activity against herpes simplex virus (2004) Antiviral Res., 64, pp. 119-126
dcterms.bibliographicCitationLi, Y., Chen, Z., RAPD: A database of recombinantly-produced antimicrobial peptides (2008) FEMS Microbiol. Lett, 289, pp. 126-129
dcterms.bibliographicCitationMagrane, M., Uniprot knowledgebase: A hub of integrated protein data (2011) Database, , 2011
dcterms.bibliographicCitationMor, A., Multifunctional host defense peptides: Antiparasitic activities (2009) FEBS J., 276, pp. 6474-6482
dcterms.bibliographicCitationNeedleman, S.B., Wunsch, C.D., A general method applicable to the search for similarities in the amino acid sequence of two proteins (1970) J. Mol. Biol., 48, pp. 443-453
dcterms.bibliographicCitationNovković, M., DADP: The database of anuran defense peptides (2012) Bioinformatics, 28, pp. 1406-1407
dcterms.bibliographicCitationPiotto, S.P., Yadamp: Yet another database of antimicrobial peptides (2012) Int. J Antimicrob. Agents, 39, pp. 346-351
dcterms.bibliographicCitationQureshi, A., Hipdb: A database of experimentally validated HIV inhibiting peptides (2013) PloS One, 8, p. e54908
dcterms.bibliographicCitationQureshi, A., Avpdb: A database of experimentally validated antiviral peptides targeting medically important viruses (2014) Nucleic Acids Res., 42, pp. D1147-D1153
dcterms.bibliographicCitationSeebah, S., Defensins knowledgebase: A manually curated database and information source focused on the defensins family of antimicrobial peptides (2007) Nucleic Acids Res., 35, pp. D265-D268
dcterms.bibliographicCitationSundararajan, V.S., DAMPD: A manually curated antimicrobial peptide database (2012) Nucleic Acids Res., 40, pp. D1108-D1112
dcterms.bibliographicCitationThéolier, J., Milkamp: A comprehensive database of antimicrobial peptides of dairy origin (2014) Dairy Sci. Technol., 94, pp. 181-193
dcterms.bibliographicCitationTorrent, M., Connecting peptide physicochemical and antimicrobial properties by a rational prediction model (2011) PloS One, 6, p. e16968
dcterms.bibliographicCitationTossi, A., Sandri, L., Molecular diversity in gene-encoded, cationic antimicrobial polypeptides (2002) Curr. Pharm. Des., 8, pp. 743-761
dcterms.bibliographicCitationVoigt, J.H., Comparison of the NCI open database with seven large chemical structural databases (2001) J. Chem. Inf. Comput. Sci, 41, pp. 702-712
dcterms.bibliographicCitationWaghu, F.H., Camp: Collection of sequences and structures of antimicrobial peptides (2014) Nucleic Acids Res., 42, pp. D1154-D1158
dcterms.bibliographicCitationWang, G., APD2: The updated antimicrobial peptide database and its application in peptide design (2009) Nucleic Acids Res., 37, pp. D933-D937
dcterms.bibliographicCitationWang, Z., Wang, G., APD: The antimicrobial peptide database (2004) Nucleic Acids Res., 32, pp. D590-D592
dcterms.bibliographicCitationWhitmore, L., Wallace, B., The peptaibol database: A database for sequences and structures of naturally occurring peptaibols (2004) Nucleic Acids Res., 32, pp. D593-D594
dcterms.bibliographicCitationWilley, J.M., Van Der Donk, W.A., Lantibiotics: Peptides of diverse structure and function (2007) Annu. Rev. Microbiol., 61, pp. 477-501
dcterms.bibliographicCitationZhao, X., Lamp: A database linking antimicrobial peptides (2013) PloS One, 8, p. e66557
datacite.rightshttp://purl.org/coar/access_right/c_abf2
oaire.resourceTypehttp://purl.org/coar/resource_type/c_6501
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.driverinfo:eu-repo/semantics/article
dc.type.hasversioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1093/bioinformatics/btv180
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.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.rights.ccAtribución-NoComercial 4.0 Internacional
dc.identifier.instnameUniversidad Tecnológica de Bolívar
dc.identifier.reponameRepositorio UTB
dc.description.notesAntimicrobial Cationic Peptides
dc.type.spaArtículo


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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.