An assessment on epitope prediction methods for protozoa genomes

Detalhes bibliográficos
Autor(a) principal: Resende, Daniela de Melo
Data de Publicação: 2012
Outros Autores: Rezende, Antônio Mauro de, Oliveira, Nesley J. D., Batista, Izabella Cristina Andrade, Oliveira, Rodrigo Corrêa de, Reis, Alexandre Barbosa, Ruiz, Jerônimo Conceição
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/7838
Resumo: FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais; CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico); Instituto René Rachou (IRR/FIOCRUZ Minas); Universidade Federal de Ouro Preto (UFOP); Programa de Pós-graduação em Ciências Farmacêuticas (CiPharma) Pontifícia Universidade Católica (PUC-MG) and Centro Universitário UNA. Grants FAPEMIG (PRONEX 503/07 and PPP APQ-04554-10), CNPq (GENOPROT 560943/2010-5 and Universal 478100/2011-6) and CAPES (PNPD 2009). JCR is also supported by the following grants: CNPq 476898/2008-0 and 476539/2010-2; FAPEMIG APQ-02382-10 and APQ-01835-10. Fellowships were provided by CNPq to ABR, RCO, RT and PCR, by CAPES to DMR and by FAPEMIG to ICAB.
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spelling Resende, Daniela de MeloRezende, Antônio Mauro deOliveira, Nesley J. D.Batista, Izabella Cristina AndradeOliveira, Rodrigo Corrêa deReis, Alexandre BarbosaRuiz, Jerônimo Conceição2014-06-25T19:28:29Z2014-06-25T19:28:29Z2012RESENDE, Daniela de Melo et al. An assessment on epitope prediction methods for protozoa genomes. BMC Bioinformatics. 2012, vol.13, pp. 309.1471-2105https://www.arca.fiocruz.br/handle/icict/7838FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais; CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico); Instituto René Rachou (IRR/FIOCRUZ Minas); Universidade Federal de Ouro Preto (UFOP); Programa de Pós-graduação em Ciências Farmacêuticas (CiPharma) Pontifícia Universidade Católica (PUC-MG) and Centro Universitário UNA. Grants FAPEMIG (PRONEX 503/07 and PPP APQ-04554-10), CNPq (GENOPROT 560943/2010-5 and Universal 478100/2011-6) and CAPES (PNPD 2009). JCR is also supported by the following grants: CNPq 476898/2008-0 and 476539/2010-2; FAPEMIG APQ-02382-10 and APQ-01835-10. Fellowships were provided by CNPq to ABR, RCO, RT and PCR, by CAPES to DMR and by FAPEMIG to ICAB.Universidade Federal de Ouro Preto. Escola de Farmácia. Laboratório de Pesquisas Clínicas. Ouro Preto, MG, Brazil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Imunologia Celular e Molecular. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/ Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, Brazil/Pontifícia Universidade Católica. Contagem, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Imunologia Celular e Molecular. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Imunologia Celular e Molecular. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Imunologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Ouro Preto. Núcleo de Pesquisas em Ciências Biológicas. Laboratório de Imunopatologia. Ouro Preto, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Centro Universitário UNA. Instituto de Ciências Biológicas e da Saúde. Belo Horizonte, MG, BrazilBackground: Epitope prediction using computational methods represents one of the most promising approaches to vaccine development. Reduction of time, cost, and the availability of completely sequenced genomes are key points and highly motivating regarding the use of reverse vaccinology. Parasites of genus Leishmania are widely spread and they are the etiologic agents of leishmaniasis. Currently, there is no efficient vaccine against this pathogen and the drug treatment is highly toxic. The lack of sufficiently large datasets of experimentally validated parasites epitopes represents a serious limitation, especially for trypanomatids genomes. In this work we highlight the predictive performances of several algorithms that were evaluated through the development of a MySQL database built with the purpose of: a) evaluating individual algorithms prediction performances and their combination for CD8+ T cell epitopes, B-cell epitopes and subcellular localization by means of AUC (Area Under Curve) performance and a threshold dependent method that employs a confusion matrix; b) integrating data from experimentally validated and in silico predicted epitopes; and c) integrating the subcellular localization predictions and experimental data. NetCTL, NetMHC, BepiPred, BCPred12, and AAP12 algorithms were used for in silico epitope prediction and WoLF PSORT, Sigcleave and TargetP for in silico subcellular localization prediction against trypanosomatid genomes.Results: A database-driven epitope prediction method was developed with built-in functions that were capable of: a) removing experimental data redundancy; b) parsing algorithms predictions and storage experimental validated and predict data; and c) evaluating algorithm performances. Results show that a better performance is achieved when the combined prediction is considered. This is particularly true for B cell epitope predictors, where the combined prediction of AAP12 and BCPred12 reached an AUC value of 0.77. For T CD8+ epitope predictors, the combined prediction of NetCTL and NetMHC reached an AUC value of 0.64. Finally, regarding the subcellular localization prediction, the best performance is achieved when the combined prediction of Sigcleave, TargetP and WoLF PSORT is used. Conclusions: Our study indicates that the combination of B cells epitope predictors is the best tool for predicting epitopes on protozoan parasites proteins. Regarding subcellular localization, the best result was obtained when the three algorithms predictions were combined. The developed pipeline is available upon request to authorsengBioMed CentralAn assessment on epitope prediction methods for protozoa genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleAntigens, Protozoan/analysisComputer SimulationEpitopes, B-Lymphocyte/geneticsEpitopes, T-Lymphocyte/analysisLeishmania/geneticsProtozoan Vaccines/geneticsProtozoan Vaccines/immunologyLeishmania/immunologyinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALAn assessment on epitope prediction methods for protozoa genomes.pdfAn assessment on epitope prediction methods for protozoa genomes.pdfapplication/pdf963088https://www.arca.fiocruz.br/bitstream/icict/7838/1/An%20assessment%20on%20epitope%20prediction%20methods%20for%20protozoa%20genomes.pdf73af49b1fbbfbf22f81e9cdcd6542987MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81914https://www.arca.fiocruz.br/bitstream/icict/7838/2/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD52TEXTAn assessment on epitope prediction methods for protozoa genomes.pdf.txtAn assessment on epitope prediction methods for protozoa genomes.pdf.txtExtracted texttext/plain52506https://www.arca.fiocruz.br/bitstream/icict/7838/5/An%20assessment%20on%20epitope%20prediction%20methods%20for%20protozoa%20genomes.pdf.txtd47c6434582e49e0edffe1dcd8083599MD55THUMBNAILAn assessment on epitope prediction methods for protozoa genomes.pdf.jpgAn assessment on epitope prediction methods for protozoa genomes.pdf.jpgGenerated Thumbnailimage/jpeg1798https://www.arca.fiocruz.br/bitstream/icict/7838/4/An%20assessment%20on%20epitope%20prediction%20methods%20for%20protozoa%20genomes.pdf.jpgccd5a770e60eac33eb249316cdb2883aMD54icict/78382018-04-06 08:48:48.936oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352018-04-06T11:48:48Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv An assessment on epitope prediction methods for protozoa genomes
title An assessment on epitope prediction methods for protozoa genomes
spellingShingle An assessment on epitope prediction methods for protozoa genomes
Resende, Daniela de Melo
Antigens, Protozoan/analysis
Computer Simulation
Epitopes, B-Lymphocyte/genetics
Epitopes, T-Lymphocyte/analysis
Leishmania/genetics
Protozoan Vaccines/genetics
Protozoan Vaccines/immunology
Leishmania/immunology
title_short An assessment on epitope prediction methods for protozoa genomes
title_full An assessment on epitope prediction methods for protozoa genomes
title_fullStr An assessment on epitope prediction methods for protozoa genomes
title_full_unstemmed An assessment on epitope prediction methods for protozoa genomes
title_sort An assessment on epitope prediction methods for protozoa genomes
author Resende, Daniela de Melo
author_facet Resende, Daniela de Melo
Rezende, Antônio Mauro de
Oliveira, Nesley J. D.
Batista, Izabella Cristina Andrade
Oliveira, Rodrigo Corrêa de
Reis, Alexandre Barbosa
Ruiz, Jerônimo Conceição
author_role author
author2 Rezende, Antônio Mauro de
Oliveira, Nesley J. D.
Batista, Izabella Cristina Andrade
Oliveira, Rodrigo Corrêa de
Reis, Alexandre Barbosa
Ruiz, Jerônimo Conceição
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Resende, Daniela de Melo
Rezende, Antônio Mauro de
Oliveira, Nesley J. D.
Batista, Izabella Cristina Andrade
Oliveira, Rodrigo Corrêa de
Reis, Alexandre Barbosa
Ruiz, Jerônimo Conceição
dc.subject.en.pt_BR.fl_str_mv Antigens, Protozoan/analysis
Computer Simulation
Epitopes, B-Lymphocyte/genetics
Epitopes, T-Lymphocyte/analysis
Leishmania/genetics
Protozoan Vaccines/genetics
Protozoan Vaccines/immunology
Leishmania/immunology
topic Antigens, Protozoan/analysis
Computer Simulation
Epitopes, B-Lymphocyte/genetics
Epitopes, T-Lymphocyte/analysis
Leishmania/genetics
Protozoan Vaccines/genetics
Protozoan Vaccines/immunology
Leishmania/immunology
description FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais; CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico); Instituto René Rachou (IRR/FIOCRUZ Minas); Universidade Federal de Ouro Preto (UFOP); Programa de Pós-graduação em Ciências Farmacêuticas (CiPharma) Pontifícia Universidade Católica (PUC-MG) and Centro Universitário UNA. Grants FAPEMIG (PRONEX 503/07 and PPP APQ-04554-10), CNPq (GENOPROT 560943/2010-5 and Universal 478100/2011-6) and CAPES (PNPD 2009). JCR is also supported by the following grants: CNPq 476898/2008-0 and 476539/2010-2; FAPEMIG APQ-02382-10 and APQ-01835-10. Fellowships were provided by CNPq to ABR, RCO, RT and PCR, by CAPES to DMR and by FAPEMIG to ICAB.
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-06-25T19:28:29Z
dc.date.available.fl_str_mv 2014-06-25T19:28:29Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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dc.identifier.citation.fl_str_mv RESENDE, Daniela de Melo et al. An assessment on epitope prediction methods for protozoa genomes. BMC Bioinformatics. 2012, vol.13, pp. 309.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/7838
dc.identifier.issn.none.fl_str_mv 1471-2105
identifier_str_mv RESENDE, Daniela de Melo et al. An assessment on epitope prediction methods for protozoa genomes. BMC Bioinformatics. 2012, vol.13, pp. 309.
1471-2105
url https://www.arca.fiocruz.br/handle/icict/7838
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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collection Repositório Institucional da FIOCRUZ (ARCA)
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