CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2022 |
| Outros Autores: | , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/54955 |
Resumo: | Central Public Health Laboratory (LCSP), Ministry of Public Health and Social Welfare MSPyBS, Asunción, Paraguay. |
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Duré, Felicita MabelSilveira, Melise ChavesSouza, Cláudio Marcos Rocha deLeão, Robson SouzaSantos, Ivson Cassiano de OliveiraAlbano, Rodolpho MattosMarques, Elizabeth AndradeAssef, Ana Paula D’Alincourt CarvalhoSilva, Fabricio Alves Barbosa da2022-10-02T16:55:10Z2022-10-02T16:55:10Z2022DURÉ, Felicita Mabel et al. CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. Frontiers in Microbiology, v. 13, Article 893474, p. 1 - 11, May 2022.1664-302Xhttps://www.arca.fiocruz.br/handle/icict/5495510.3389/fmicb.2022.893474engFrontiers MediaBactériaAplicativo da webPipelineBioinformáticaGenomaResistência antimicrobianaBacteriaWeb applicationPipelineBioinformaticsGenomeAntimicrobial resistanceCABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleCentral Public Health Laboratory (LCSP), Ministry of Public Health and Social Welfare MSPyBS, Asunción, Paraguay.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ, Brasil.Universidade do Estado do Rio de Janeiro. Instituto de Biologia Roberto de Alcântara Gomes. Departamento de Bioquímica. Rio de Janeiro, RJ, Brasil / Universidade do Estado do Rio de Janeiro. Faculdade de Ciências Médicas. Departamento de Microbiologia, Imunologia e Parasitologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ, Brasil.Universidade do Estado do Rio de Janeiro. Instituto de Biologia Roberto de Alcântara Gomes. Departamento de Bioquímica. Rio de Janeiro, RJ, BrasilUniversidade do Estado do Rio de Janeiro. Instituto de Biologia Roberto de Alcântara Gomes. Departamento de Bioquímica. Rio de Janeiro, RJ, Brasil / Universidade do Estado do Rio de Janeiro. Faculdade de Ciências Médicas. Departamento de Microbiologia, Imunologia e Parasitologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.Due to recent developments in NGS technologies, genome sequencing is generating large volumes of new data containing a wealth of biological information. Understanding sequenced genomes in a biologically meaningful way and delineating their functional and metabolic landscapes is a first-level challenge. Considering the global antimicrobial resistance (AMR) problem, investments to expand surveillance and improve existing genome analysis technologies are pressing. In addition, the speed at which new genomic data is generated surpasses our capacity to analyze it with available bioinformatics methods, thus creating a need to develop new, user-friendly and comprehensive analytical tools. To this end, we propose a new web application, CABGen,1 developed with open-source software. CABGen allows storing, organizing, analyzing, and interpreting bioinformatics data in a friendly, scalable, easy-to-use environment and can process data from bacterial isolates of different species and origins. CABGen has three modules: Upload Sequences, Analyze Sequences, and Verify Results. Functionalities include coverage estimation, species identification, de novo genome assembly, and assembly quality, genome annotation, MLST mapping, searches for genes related to AMR, virulence, and plasmids, and detection of point mutations in specific AMR genes. Visualization tools are also available, greatly facilitating the handling of biological data. The reports include those results that are clinically relevant. To illustrate the use of CABGen, whole-genome shotgun data from 181 bacterial isolates of different species collected in 5 Brazilian regions between 2018 and 2020 were uploaded and submitted to the platform’s modules.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/54955/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMeliseSilveira_ClaudioSouza_etal_IOC_2022.pdfMeliseSilveira_ClaudioSouza_etal_IOC_2022.pdfapplication/pdf2309838https://www.arca.fiocruz.br/bitstream/icict/54955/2/MeliseSilveira_ClaudioSouza_etal_IOC_2022.pdf5254150280485c2a77e7d8acdee86b83MD52icict/549552023-09-04 11:30:06.051oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-04T14:30:06Repositório Institucional da FIOCRUZ (ARCA) - 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| dc.title.en_US.fl_str_mv |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| title |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| spellingShingle |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes Duré, Felicita Mabel Bactéria Aplicativo da web Pipeline Bioinformática Genoma Resistência antimicrobiana Bacteria Web application Pipeline Bioinformatics Genome Antimicrobial resistance |
| title_short |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| title_full |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| title_fullStr |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| title_full_unstemmed |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| title_sort |
CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes |
| author |
Duré, Felicita Mabel |
| author_facet |
Duré, Felicita Mabel Silveira, Melise Chaves Souza, Cláudio Marcos Rocha de Leão, Robson Souza Santos, Ivson Cassiano de Oliveira Albano, Rodolpho Mattos Marques, Elizabeth Andrade Assef, Ana Paula D’Alincourt Carvalho Silva, Fabricio Alves Barbosa da |
| author_role |
author |
| author2 |
Silveira, Melise Chaves Souza, Cláudio Marcos Rocha de Leão, Robson Souza Santos, Ivson Cassiano de Oliveira Albano, Rodolpho Mattos Marques, Elizabeth Andrade Assef, Ana Paula D’Alincourt Carvalho Silva, Fabricio Alves Barbosa da |
| author2_role |
author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Duré, Felicita Mabel Silveira, Melise Chaves Souza, Cláudio Marcos Rocha de Leão, Robson Souza Santos, Ivson Cassiano de Oliveira Albano, Rodolpho Mattos Marques, Elizabeth Andrade Assef, Ana Paula D’Alincourt Carvalho Silva, Fabricio Alves Barbosa da |
| dc.subject.other.en_US.fl_str_mv |
Bactéria Aplicativo da web Pipeline Bioinformática Genoma Resistência antimicrobiana |
| topic |
Bactéria Aplicativo da web Pipeline Bioinformática Genoma Resistência antimicrobiana Bacteria Web application Pipeline Bioinformatics Genome Antimicrobial resistance |
| dc.subject.en.en_US.fl_str_mv |
Bacteria Web application Pipeline Bioinformatics Genome Antimicrobial resistance |
| description |
Central Public Health Laboratory (LCSP), Ministry of Public Health and Social Welfare MSPyBS, Asunción, Paraguay. |
| publishDate |
2022 |
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2022-10-02T16:55:10Z |
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2022-10-02T16:55:10Z |
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2022 |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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DURÉ, Felicita Mabel et al. CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. Frontiers in Microbiology, v. 13, Article 893474, p. 1 - 11, May 2022. |
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https://www.arca.fiocruz.br/handle/icict/54955 |
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1664-302X |
| dc.identifier.doi.none.fl_str_mv |
10.3389/fmicb.2022.893474 |
| identifier_str_mv |
DURÉ, Felicita Mabel et al. CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. Frontiers in Microbiology, v. 13, Article 893474, p. 1 - 11, May 2022. 1664-302X 10.3389/fmicb.2022.893474 |
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Frontiers Media |
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Frontiers Media |
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