Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set
Autor(a) principal: | |
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Data de Publicação: | 2009 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.cam.2008.03.018 http://hdl.handle.net/11449/9882 |
Resumo: | The taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved. |
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Repositório Institucional da UNESP |
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spelling |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data setCluster AnalysisBrodyrhizobium GenusbioinformaticsThe taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved.Univ São Paulo, Dept Elect Engn, BR-13566590 São Carlos, SP, BrazilGoias Fed Univ, Catalao, BrazilState Univ São Paulo, Dept Elect Engn, Ilha Solteira, BrazilSoil Biotechnol Lab, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Soja, Londrina, BrazilState Univ São Paulo, Dept Elect Engn, Ilha Solteira, BrazilElsevier B.V.Universidade de São Paulo (USP)Universidade Federal de Goiás (UFG)Universidade Estadual Paulista (Unesp)Soil Biotechnol LabMilagre, S. T.Maciel, C. D.Shinoda, Ailton Akira [UNESP]Hungria, M.Almeida, J. R. B.2014-05-20T13:29:21Z2014-05-20T13:29:21Z2009-05-15info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article308-319application/pdfhttp://dx.doi.org/10.1016/j.cam.2008.03.018Journal of Computational and Applied Mathematics. Amsterdam: Elsevier B.V., v. 227, n. 2, p. 308-319, 2009.0377-0427http://hdl.handle.net/11449/988210.1016/j.cam.2008.03.018WOS:000265170000009WOS000265170000009.pdf9387430150792972Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Computational and Applied Mathematics1.6320,938info:eu-repo/semantics/openAccess2024-07-04T19:06:25Zoai:repositorio.unesp.br:11449/9882Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:12:27.095532Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
title |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
spellingShingle |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set Milagre, S. T. Cluster Analysis Brodyrhizobium Genus bioinformatics |
title_short |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
title_full |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
title_fullStr |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
title_full_unstemmed |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
title_sort |
Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set |
author |
Milagre, S. T. |
author_facet |
Milagre, S. T. Maciel, C. D. Shinoda, Ailton Akira [UNESP] Hungria, M. Almeida, J. R. B. |
author_role |
author |
author2 |
Maciel, C. D. Shinoda, Ailton Akira [UNESP] Hungria, M. Almeida, J. R. B. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Federal de Goiás (UFG) Universidade Estadual Paulista (Unesp) Soil Biotechnol Lab |
dc.contributor.author.fl_str_mv |
Milagre, S. T. Maciel, C. D. Shinoda, Ailton Akira [UNESP] Hungria, M. Almeida, J. R. B. |
dc.subject.por.fl_str_mv |
Cluster Analysis Brodyrhizobium Genus bioinformatics |
topic |
Cluster Analysis Brodyrhizobium Genus bioinformatics |
description |
The taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved. |
publishDate |
2009 |
dc.date.none.fl_str_mv |
2009-05-15 2014-05-20T13:29:21Z 2014-05-20T13:29:21Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.cam.2008.03.018 Journal of Computational and Applied Mathematics. Amsterdam: Elsevier B.V., v. 227, n. 2, p. 308-319, 2009. 0377-0427 http://hdl.handle.net/11449/9882 10.1016/j.cam.2008.03.018 WOS:000265170000009 WOS000265170000009.pdf 9387430150792972 |
url |
http://dx.doi.org/10.1016/j.cam.2008.03.018 http://hdl.handle.net/11449/9882 |
identifier_str_mv |
Journal of Computational and Applied Mathematics. Amsterdam: Elsevier B.V., v. 227, n. 2, p. 308-319, 2009. 0377-0427 10.1016/j.cam.2008.03.018 WOS:000265170000009 WOS000265170000009.pdf 9387430150792972 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Computational and Applied Mathematics 1.632 0,938 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
308-319 application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier B.V. |
publisher.none.fl_str_mv |
Elsevier B.V. |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129032931246080 |