Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/200531 |
Resumo: | Dendrograms are a way to represent relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic material of choice for the sequence alignments (all the genes or sets of genes) results in distinct inferred dendrograms. In this work, we evaluate differences between dendrograms reconstructed with different methodologies and for different sets of organisms chosen at random from a much larger set. A statistical analysis is performed to estimate fluctuations between the results obtained from the different methodologies that allows us to validate a systematic approach, based on the comparison of the organisms’ metabolic networks for inferring dendrograms. This has the advantage that it allows the comparison of organisms very far away in the evolutionary tree even if they have no known ortholog gene in common. Our results show that dendrograms built using information from metabolic networks are similar to the standard sequence-based dendrograms and can be a complement to them |
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Gamermann, DanielMontagud Aquino, ArnauConejero, J. AlbertoFernández de Córdoba, PedroUrchueguía Schölzel, Javier Fermín2019-10-11T03:55:47Z20191932-6203http://hdl.handle.net/10183/200531001101993Dendrograms are a way to represent relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic material of choice for the sequence alignments (all the genes or sets of genes) results in distinct inferred dendrograms. In this work, we evaluate differences between dendrograms reconstructed with different methodologies and for different sets of organisms chosen at random from a much larger set. A statistical analysis is performed to estimate fluctuations between the results obtained from the different methodologies that allows us to validate a systematic approach, based on the comparison of the organisms’ metabolic networks for inferring dendrograms. This has the advantage that it allows the comparison of organisms very far away in the evolutionary tree even if they have no known ortholog gene in common. Our results show that dendrograms built using information from metabolic networks are similar to the standard sequence-based dendrograms and can be a complement to themapplication/pdfengPLoS ONE. San Francisco. Vol. 14, no. 9 (Sept. 2019), e0221631, 13 p.Biofisica celularDinamica celularGenéticaBiologiaLarge scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstructionEstrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSTEXT001101993.pdf.txt001101993.pdf.txtExtracted Texttext/plain43475http://www.lume.ufrgs.br/bitstream/10183/200531/2/001101993.pdf.txt6ff1553d33ba77326452eed273a49defMD52ORIGINAL001101993.pdfTexto completo (inglês)application/pdf1071014http://www.lume.ufrgs.br/bitstream/10183/200531/1/001101993.pdf68d56ed52b72059278e77e7242dbd1e7MD5110183/2005312023-07-15 03:28:27.181871oai:www.lume.ufrgs.br:10183/200531Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-07-15T06:28:27Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
title |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
spellingShingle |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction Gamermann, Daniel Biofisica celular Dinamica celular Genética Biologia |
title_short |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
title_full |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
title_fullStr |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
title_full_unstemmed |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
title_sort |
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction |
author |
Gamermann, Daniel |
author_facet |
Gamermann, Daniel Montagud Aquino, Arnau Conejero, J. Alberto Fernández de Córdoba, Pedro Urchueguía Schölzel, Javier Fermín |
author_role |
author |
author2 |
Montagud Aquino, Arnau Conejero, J. Alberto Fernández de Córdoba, Pedro Urchueguía Schölzel, Javier Fermín |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Gamermann, Daniel Montagud Aquino, Arnau Conejero, J. Alberto Fernández de Córdoba, Pedro Urchueguía Schölzel, Javier Fermín |
dc.subject.por.fl_str_mv |
Biofisica celular Dinamica celular Genética Biologia |
topic |
Biofisica celular Dinamica celular Genética Biologia |
description |
Dendrograms are a way to represent relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic material of choice for the sequence alignments (all the genes or sets of genes) results in distinct inferred dendrograms. In this work, we evaluate differences between dendrograms reconstructed with different methodologies and for different sets of organisms chosen at random from a much larger set. A statistical analysis is performed to estimate fluctuations between the results obtained from the different methodologies that allows us to validate a systematic approach, based on the comparison of the organisms’ metabolic networks for inferring dendrograms. This has the advantage that it allows the comparison of organisms very far away in the evolutionary tree even if they have no known ortholog gene in common. Our results show that dendrograms built using information from metabolic networks are similar to the standard sequence-based dendrograms and can be a complement to them |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-10-11T03:55:47Z |
dc.date.issued.fl_str_mv |
2019 |
dc.type.driver.fl_str_mv |
Estrangeiro info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10183/200531 |
dc.identifier.issn.pt_BR.fl_str_mv |
1932-6203 |
dc.identifier.nrb.pt_BR.fl_str_mv |
001101993 |
identifier_str_mv |
1932-6203 001101993 |
url |
http://hdl.handle.net/10183/200531 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
PLoS ONE. San Francisco. Vol. 14, no. 9 (Sept. 2019), e0221631, 13 p. |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
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reponame:Repositório Institucional da UFRGS instname:Universidade Federal do Rio Grande do Sul (UFRGS) instacron:UFRGS |
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Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS) |
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