A gene based bacterial whole genome comparison toolkit.

Detalhes bibliográficos
Autor(a) principal: Digiampietri, Luciano Antonio
Data de Publicação: 2019
Outros Autores: Pereira, Vivian Mayumi Yamassak, Santos Júnior, Geraldo Jose dos, Leite, Giovani de Sousa, Wagner, Priscilla Koch, Moreira, Leandro Marcio, Santiago, Caio Rafael do Nascimento
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFOP
Texto Completo: http://www.repositorio.ufop.br/handle/123456789/12033
https://doi.org/10.22456/2175-2745.84814
Resumo: Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.
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spelling Digiampietri, Luciano AntonioPereira, Vivian Mayumi YamassakSantos Júnior, Geraldo Jose dosLeite, Giovani de SousaWagner, Priscilla KochMoreira, Leandro MarcioSantiago, Caio Rafael do Nascimento2020-04-07T15:55:14Z2020-04-07T15:55:14Z2019DIGIAMPIETRI, L. A. et al. A gene based bacterial whole genome comparison toolkit. Revista de Informática Teórica e Aplicada: RITA, v. 26, n.1, p. 36-46, 2019. Disponível em: <https://seer.ufrgs.br/rita/article/view/RITA-VOL26-NR1-36>. Acesso em: 10 fev. 2020.2175-2745http://www.repositorio.ufop.br/handle/123456789/12033https://doi.org/10.22456/2175-2745.84814Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.Grande parte das analises realizadas na biologia computacional é feita comparando características genômicas. Os alinhamentos de nucleotídeos e de aminoácidos são frequentemente usados na identificação de funções gênicas e na comparação de genomas. Apesar de seu uso generalizado, há limitações em suas capacidades de analise que precisam ser consideradas, mas são frequentemente negligenciadas ou desconhecidas por muitos pesquisadores. Este artigo apresenta um conjunto de ferramentas de comparação de genomas completos baseado em genes que pode ser usado não somente como uma maneira alternativa e mais robusta de comparar um conjunto de genomas completos, mas também para entender as vantagens e desvantagens do uso do alinhamento local de sequencias neste tipo de comparação. Um estudo de caso foi realizado considerando quinze genomas completos do gênero Xanthomonas. Os resultados foram comparados com a filogenia produzida utilizando a proteína 16S rRNA-processing protein RimM e alguns limiares para o uso de alinhamentos de sequencias neste tipo de analise foram discutidos.This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. Fonte: o próprio artigo.info:eu-repo/semantics/openAccessBioinformaticsPhylogenyPangenomeGenome visualizationA gene based bacterial whole genome comparison toolkit.Um conjunto de ferramentas para a comparação de genomas completos de bactérias baseada em genes.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleengreponame:Repositório Institucional da UFOPinstname:Universidade Federal de Ouro Preto (UFOP)instacron:UFOPLICENSElicense.txtlicense.txttext/plain; charset=utf-8924http://www.repositorio.ufop.br/bitstream/123456789/12033/2/license.txt62604f8d955274beb56c80ce1ee5dcaeMD52ORIGINALARTIGO_GeneBasedBacterial.pdfARTIGO_GeneBasedBacterial.pdfapplication/pdf942225http://www.repositorio.ufop.br/bitstream/123456789/12033/1/ARTIGO_GeneBasedBacterial.pdff293831f4a4fc68b6890fb943cc2a530MD51123456789/120332020-04-07 11:55:14.474oai:localhost: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ório InstitucionalPUBhttp://www.repositorio.ufop.br/oai/requestrepositorio@ufop.edu.bropendoar:32332020-04-07T15:55:14Repositório Institucional da UFOP - Universidade Federal de Ouro Preto (UFOP)false
dc.title.pt_BR.fl_str_mv A gene based bacterial whole genome comparison toolkit.
dc.title.alternative.pt_BR.fl_str_mv Um conjunto de ferramentas para a comparação de genomas completos de bactérias baseada em genes.
title A gene based bacterial whole genome comparison toolkit.
spellingShingle A gene based bacterial whole genome comparison toolkit.
Digiampietri, Luciano Antonio
Bioinformatics
Phylogeny
Pangenome
Genome visualization
title_short A gene based bacterial whole genome comparison toolkit.
title_full A gene based bacterial whole genome comparison toolkit.
title_fullStr A gene based bacterial whole genome comparison toolkit.
title_full_unstemmed A gene based bacterial whole genome comparison toolkit.
title_sort A gene based bacterial whole genome comparison toolkit.
author Digiampietri, Luciano Antonio
author_facet Digiampietri, Luciano Antonio
Pereira, Vivian Mayumi Yamassak
Santos Júnior, Geraldo Jose dos
Leite, Giovani de Sousa
Wagner, Priscilla Koch
Moreira, Leandro Marcio
Santiago, Caio Rafael do Nascimento
author_role author
author2 Pereira, Vivian Mayumi Yamassak
Santos Júnior, Geraldo Jose dos
Leite, Giovani de Sousa
Wagner, Priscilla Koch
Moreira, Leandro Marcio
Santiago, Caio Rafael do Nascimento
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Digiampietri, Luciano Antonio
Pereira, Vivian Mayumi Yamassak
Santos Júnior, Geraldo Jose dos
Leite, Giovani de Sousa
Wagner, Priscilla Koch
Moreira, Leandro Marcio
Santiago, Caio Rafael do Nascimento
dc.subject.por.fl_str_mv Bioinformatics
Phylogeny
Pangenome
Genome visualization
topic Bioinformatics
Phylogeny
Pangenome
Genome visualization
description Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.
publishDate 2019
dc.date.issued.fl_str_mv 2019
dc.date.accessioned.fl_str_mv 2020-04-07T15:55:14Z
dc.date.available.fl_str_mv 2020-04-07T15:55:14Z
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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status_str publishedVersion
dc.identifier.citation.fl_str_mv DIGIAMPIETRI, L. A. et al. A gene based bacterial whole genome comparison toolkit. Revista de Informática Teórica e Aplicada: RITA, v. 26, n.1, p. 36-46, 2019. Disponível em: <https://seer.ufrgs.br/rita/article/view/RITA-VOL26-NR1-36>. Acesso em: 10 fev. 2020.
dc.identifier.uri.fl_str_mv http://www.repositorio.ufop.br/handle/123456789/12033
dc.identifier.issn.none.fl_str_mv 2175-2745
dc.identifier.doi.pt_BR.fl_str_mv https://doi.org/10.22456/2175-2745.84814
identifier_str_mv DIGIAMPIETRI, L. A. et al. A gene based bacterial whole genome comparison toolkit. Revista de Informática Teórica e Aplicada: RITA, v. 26, n.1, p. 36-46, 2019. Disponível em: <https://seer.ufrgs.br/rita/article/view/RITA-VOL26-NR1-36>. Acesso em: 10 fev. 2020.
2175-2745
url http://www.repositorio.ufop.br/handle/123456789/12033
https://doi.org/10.22456/2175-2745.84814
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFOP
instname:Universidade Federal de Ouro Preto (UFOP)
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instacron_str UFOP
institution UFOP
reponame_str Repositório Institucional da UFOP
collection Repositório Institucional da UFOP
bitstream.url.fl_str_mv http://www.repositorio.ufop.br/bitstream/123456789/12033/2/license.txt
http://www.repositorio.ufop.br/bitstream/123456789/12033/1/ARTIGO_GeneBasedBacterial.pdf
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