Evaluation of genome similarities using independent components

Detalhes bibliográficos
Autor(a) principal: Sáfadi, Thelma
Data de Publicação: 2020
Outros Autores: Ferreira, Leila Maria
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFLA
Texto Completo: http://repositorio.ufla.br/jspui/handle/1/46660
Resumo: We propose the use of independent component analysis to find similarities of genomes. Considering different numbers of independent components, the complete linkage method was used to identify groups based on the estimated coefficients of the mixing matrix. The sequences analyzed correspond to the strains of the Mycobacterium tuberculosis genome, ten sequences were analyzed, obtained from the National Center for Biotechnology Information (NCBI, 2017). The GC-content of each sequence was evaluated using a sliding window of 10,000 bases. The clustering analysis using the independent components of the analyzed sequences was essential to verify the dissimilarity of the sequences.
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spelling Evaluation of genome similarities using independent componentsGC-contentMycobacterium tuberculosis genomesCluster analysisGenomas de Mycobacterium tuberculosisAnálise de clusterWe propose the use of independent component analysis to find similarities of genomes. Considering different numbers of independent components, the complete linkage method was used to identify groups based on the estimated coefficients of the mixing matrix. The sequences analyzed correspond to the strains of the Mycobacterium tuberculosis genome, ten sequences were analyzed, obtained from the National Center for Biotechnology Information (NCBI, 2017). The GC-content of each sequence was evaluated using a sliding window of 10,000 bases. The clustering analysis using the independent components of the analyzed sequences was essential to verify the dissimilarity of the sequences.Universidade Federal de Lavras2021-07-06T16:51:10Z2021-07-06T16:51:10Z2020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfSÁFADI, T.; FERREIRA, L. M. Evaluation of genome similarities using independent components. Revista Brasileira de Biometria, Lavras, v. 38, n. 1, p. 92-101, 2020.http://repositorio.ufla.br/jspui/handle/1/46660Revista Brasileira de Biometriareponame:Repositório Institucional da UFLAinstname:Universidade Federal de Lavras (UFLA)instacron:UFLAAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessSáfadi, ThelmaFerreira, Leila Mariaeng2023-05-26T19:36:31Zoai:localhost:1/46660Repositório InstitucionalPUBhttp://repositorio.ufla.br/oai/requestnivaldo@ufla.br || repositorio.biblioteca@ufla.bropendoar:2023-05-26T19:36:31Repositório Institucional da UFLA - Universidade Federal de Lavras (UFLA)false
dc.title.none.fl_str_mv Evaluation of genome similarities using independent components
title Evaluation of genome similarities using independent components
spellingShingle Evaluation of genome similarities using independent components
Sáfadi, Thelma
GC-content
Mycobacterium tuberculosis genomes
Cluster analysis
Genomas de Mycobacterium tuberculosis
Análise de cluster
title_short Evaluation of genome similarities using independent components
title_full Evaluation of genome similarities using independent components
title_fullStr Evaluation of genome similarities using independent components
title_full_unstemmed Evaluation of genome similarities using independent components
title_sort Evaluation of genome similarities using independent components
author Sáfadi, Thelma
author_facet Sáfadi, Thelma
Ferreira, Leila Maria
author_role author
author2 Ferreira, Leila Maria
author2_role author
dc.contributor.author.fl_str_mv Sáfadi, Thelma
Ferreira, Leila Maria
dc.subject.por.fl_str_mv GC-content
Mycobacterium tuberculosis genomes
Cluster analysis
Genomas de Mycobacterium tuberculosis
Análise de cluster
topic GC-content
Mycobacterium tuberculosis genomes
Cluster analysis
Genomas de Mycobacterium tuberculosis
Análise de cluster
description We propose the use of independent component analysis to find similarities of genomes. Considering different numbers of independent components, the complete linkage method was used to identify groups based on the estimated coefficients of the mixing matrix. The sequences analyzed correspond to the strains of the Mycobacterium tuberculosis genome, ten sequences were analyzed, obtained from the National Center for Biotechnology Information (NCBI, 2017). The GC-content of each sequence was evaluated using a sliding window of 10,000 bases. The clustering analysis using the independent components of the analyzed sequences was essential to verify the dissimilarity of the sequences.
publishDate 2020
dc.date.none.fl_str_mv 2020
2021-07-06T16:51:10Z
2021-07-06T16:51:10Z
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 SÁFADI, T.; FERREIRA, L. M. Evaluation of genome similarities using independent components. Revista Brasileira de Biometria, Lavras, v. 38, n. 1, p. 92-101, 2020.
http://repositorio.ufla.br/jspui/handle/1/46660
identifier_str_mv SÁFADI, T.; FERREIRA, L. M. Evaluation of genome similarities using independent components. Revista Brasileira de Biometria, Lavras, v. 38, n. 1, p. 92-101, 2020.
url http://repositorio.ufla.br/jspui/handle/1/46660
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidade Federal de Lavras
publisher.none.fl_str_mv Universidade Federal de Lavras
dc.source.none.fl_str_mv Revista Brasileira de Biometria
reponame:Repositório Institucional da UFLA
instname:Universidade Federal de Lavras (UFLA)
instacron:UFLA
instname_str Universidade Federal de Lavras (UFLA)
instacron_str UFLA
institution UFLA
reponame_str Repositório Institucional da UFLA
collection Repositório Institucional da UFLA
repository.name.fl_str_mv Repositório Institucional da UFLA - Universidade Federal de Lavras (UFLA)
repository.mail.fl_str_mv nivaldo@ufla.br || repositorio.biblioteca@ufla.br
_version_ 1815439368225030144

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