Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
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 nonredund...
- Autores:
- Tipo de recurso:
- Fecha de publicación:
- 2015
- Institución:
- Universidad Tecnológica de Bolívar
- Repositorio:
- Repositorio Institucional UTB
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.utb.edu.co:20.500.12585/8759
- Acceso en línea:
- https://hdl.handle.net/20.500.12585/8759
- Palabra clave:
- Antimicrobial cationic peptide
Algorithm
Chemistry
Human
Nucleic acid database
Procedures
Protein database
Sequence analysis
Software
Algorithms
Antimicrobial cationic peptides
Databases, Nucleic Acid
Databases, Protein
Humans
Sequence Analysis, Protein
Software
- Rights
- openAccess
- License
- http://creativecommons.org/licenses/by-nc-nd/4.0/
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Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| title |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| spellingShingle |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences Antimicrobial cationic peptide Algorithm Chemistry Human Nucleic acid database Procedures Protein database Sequence analysis Software Algorithms Antimicrobial cationic peptides Databases, Nucleic Acid Databases, Protein Humans Sequence Analysis, Protein Software |
| title_short |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| title_full |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| title_fullStr |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| title_full_unstemmed |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| title_sort |
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences |
| dc.subject.keywords.none.fl_str_mv |
Antimicrobial cationic peptide Algorithm Chemistry Human Nucleic acid database Procedures Protein database Sequence analysis Software Algorithms Antimicrobial cationic peptides Databases, Nucleic Acid Databases, Protein Humans Sequence Analysis, Protein Software |
| topic |
Antimicrobial cationic peptide Algorithm Chemistry Human Nucleic acid database Procedures Protein database Sequence analysis Software Algorithms Antimicrobial cationic peptides Databases, Nucleic Acid Databases, Protein Humans Sequence Analysis, Protein Software |
| description |
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 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. |
| publishDate |
2015 |
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2015 |
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2019-11-06T19:05:19Z |
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2019-11-06T19:05:19Z |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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Artículo |
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publishedVersion |
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Bioinformatics; Vol. 31, Núm. 15; pp. 2553-2559 |
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1367-4803 |
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https://hdl.handle.net/20.500.12585/8759 |
| dc.identifier.doi.none.fl_str_mv |
10.1093/bioinformatics/btv180 |
| dc.identifier.instname.none.fl_str_mv |
Universidad Tecnológica de Bolívar |
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Repositorio UTB |
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Bioinformatics; Vol. 31, Núm. 15; pp. 2553-2559 1367-4803 10.1093/bioinformatics/btv180 Universidad Tecnológica de Bolívar Repositorio UTB |
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https://hdl.handle.net/20.500.12585/8759 |
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eng |
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eng |
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http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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info:eu-repo/semantics/openAccess |
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Atribución-NoComercial 4.0 Internacional |
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http://creativecommons.org/licenses/by-nc-nd/4.0/ Atribución-NoComercial 4.0 Internacional http://purl.org/coar/access_right/c_abf2 |
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openAccess |
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Recurso electrónico |
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application/pdf |
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Oxford University Press |
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Oxford University Press |
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2019-11-06T19:05:19Z2019-11-06T19:05:19Z2015Bioinformatics; Vol. 31, Núm. 15; pp. 2553-25591367-4803https://hdl.handle.net/20.500.12585/875910.1093/bioinformatics/btv180Universidad Tecnológica de BolívarRepositorio UTBMotivation: 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.Antimicrobial Cationic PeptidesRecurso electrónicoapplication/pdfengOxford University Presshttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessAtribución-NoComercial 4.0 Internacionalhttp://purl.org/coar/access_right/c_abf2https://www2.scopus.com/inward/record.uri?eid=2-s2.0-84943601205&doi=10.1093%2fbioinformatics%2fbtv180&partnerID=40&md5=141f38519649235606ce49338df9709eScopus 56035076700Scopus 55665599200Scopus 56897175400Scopus 56035437800Scopus 7102811634Scopus 55363486500Scopus 56896521800Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequencesinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb1Antimicrobial cationic peptideAlgorithmChemistryHumanNucleic acid databaseProceduresProtein databaseSequence analysisSoftwareAlgorithmsAntimicrobial cationic peptidesDatabases, Nucleic AcidDatabases, ProteinHumansSequence Analysis, ProteinSoftwareMarrero-Ponce, Y.Marrero-Ponce, Y.Tellez-Ibarra, R.Llorente-Quesada, M.T.Salgado, J.Barigye, S.J.Liu, J.Brahmachary, M., Antimic: A database of antimicrobial sequences (2004) Nucleic Acids Res., 32, pp. D586-D589Chugh, J., Wallace, B., Peptaibols: Models for ion channels (2001) Biochem. Soc. Trans., 29, pp. 565-570Cotter, P.D., Bacteriocins: Developing innate immunity for food (2005) Nat. Rev. Microbiol., 3, pp. 777-788De Jong, A., Bagel2: Mining for bacteriocins in genomic data (2010) Nucleic Acids Res., 38, pp. W647-W651Engler, A.C., Emerging trends in macromolecular antimicrobials to fight multi-drug-resistant infections (2012) Nano Today, 7, pp. 201-222Fjell, C.D., AMPer: A database and an automated discovery tool for antimicrobial peptides (2007) Bioinformatics, 23, pp. 1148-1155Fjell, C.D., Designing antimicrobial peptides: Form follows function (2012) Nat. Rev. Drug Discov., 11, pp. 37-51Ganz, T., Defensins: Antimicrobial peptides of innate immunity (2003) Nat. Rev. Immunol., 3, pp. 710-720Gaspar, D., From antimicrobial to anticancer peptides (2013) A Review. Front. Microbiol., 4, p. 294Gogoladze, G., DBAASP: Database of antimicrobial activity and structure of peptides (2014) FEMS Microbiol. Lett., 357, pp. 63-68Gueguen, Y., Penbase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature (2006) Dev. Comp. Immunol., 30, pp. 283-288Hammami, R., Phytamp: A database dedicated to antimicrobial plant peptides (2009) Nucleic Acids Res., 37, pp. D963-D968Hammami, R., Bactibase second release: A database and tool platform for bacteriocin characterization (2010) BMC Microbiol., 10, p. 22Holland, R.C., Biojava: An open-source framework for bioinformatics (2008) Bioinformatics, 24, pp. 2096-2097Holm, L., Sander, C., Removing near-neighbour redundancy from large protein sequence collections (1998) Bioinformatics, 14, pp. 423-429Jenssen, H., A wide range of medium-sized, highly cationic, a-helical peptides show antiviral activity against herpes simplex virus (2004) Antiviral Res., 64, pp. 119-126Li, Y., Chen, Z., RAPD: A database of recombinantly-produced antimicrobial peptides (2008) FEMS Microbiol. Lett, 289, pp. 126-129Magrane, M., Uniprot knowledgebase: A hub of integrated protein data (2011) Database, , 2011Mor, A., Multifunctional host defense peptides: Antiparasitic activities (2009) FEBS J., 276, pp. 6474-6482Needleman, 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. 443-453Novković, M., DADP: The database of anuran defense peptides (2012) Bioinformatics, 28, pp. 1406-1407Piotto, S.P., Yadamp: Yet another database of antimicrobial peptides (2012) Int. J Antimicrob. Agents, 39, pp. 346-351Qureshi, A., Hipdb: A database of experimentally validated HIV inhibiting peptides (2013) PloS One, 8, p. e54908Qureshi, A., Avpdb: A database of experimentally validated antiviral peptides targeting medically important viruses (2014) Nucleic Acids Res., 42, pp. D1147-D1153Seebah, 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-D268Sundararajan, V.S., DAMPD: A manually curated antimicrobial peptide database (2012) Nucleic Acids Res., 40, pp. D1108-D1112Théolier, J., Milkamp: A comprehensive database of antimicrobial peptides of dairy origin (2014) Dairy Sci. Technol., 94, pp. 181-193Torrent, M., Connecting peptide physicochemical and antimicrobial properties by a rational prediction model (2011) PloS One, 6, p. e16968Tossi, A., Sandri, L., Molecular diversity in gene-encoded, cationic antimicrobial polypeptides (2002) Curr. Pharm. Des., 8, pp. 743-761Voigt, J.H., Comparison of the NCI open database with seven large chemical structural databases (2001) J. Chem. Inf. Comput. Sci, 41, pp. 702-712Waghu, F.H., Camp: Collection of sequences and structures of antimicrobial peptides (2014) Nucleic Acids Res., 42, pp. D1154-D1158Wang, G., APD2: The updated antimicrobial peptide database and its application in peptide design (2009) Nucleic Acids Res., 37, pp. D933-D937Wang, Z., Wang, G., APD: The antimicrobial peptide database (2004) Nucleic Acids Res., 32, pp. D590-D592Whitmore, L., Wallace, B., The peptaibol database: A database for sequences and structures of naturally occurring peptaibols (2004) Nucleic Acids Res., 32, pp. D593-D594Willey, J.M., Van Der Donk, W.A., Lantibiotics: Peptides of diverse structure and function (2007) Annu. Rev. Microbiol., 61, pp. 477-501Zhao, X., Lamp: A database linking antimicrobial peptides (2013) PloS One, 8, p. e66557http://purl.org/coar/resource_type/c_6501ORIGINALDOI10_1093bioinformaticsbtv180.pdfapplication/pdf296423https://repositorio.utb.edu.co/bitstream/20.500.12585/8759/1/DOI10_1093bioinformaticsbtv180.pdfb597c548ffda4d59dc2eb405bbc7ebd0MD51TEXTDOI10_1093bioinformaticsbtv180.pdf.txtDOI10_1093bioinformaticsbtv180.pdf.txtExtracted texttext/plain38711https://repositorio.utb.edu.co/bitstream/20.500.12585/8759/4/DOI10_1093bioinformaticsbtv180.pdf.txte675d00a29cec4b65a1014ce0b56c6f8MD54THUMBNAILDOI10_1093bioinformaticsbtv180.pdf.jpgDOI10_1093bioinformaticsbtv180.pdf.jpgGenerated Thumbnailimage/jpeg82812https://repositorio.utb.edu.co/bitstream/20.500.12585/8759/5/DOI10_1093bioinformaticsbtv180.pdf.jpg1c2091101bfcc539d6a9582b37e1780eMD5520.500.12585/8759oai:repositorio.utb.edu.co:20.500.12585/87592023-05-26 16:14:27.37Repositorio Institucional UTBrepositorioutb@utb.edu.co |