A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10773/25204 |
Resumo: | In the present paper, our main goal is focused in developing fast algorithms for human mtDNA sequence analyses, requiring minimum and explicit assumptions on mutation models and evolutionary pathways. We propose a new approach based on a construction of Dawson, a technique based on the ordering of the variable sites. In this approach, the first step corresponds to the computation of the order of the positions according to their capacity to separate the sequences into dichotomous groups. Aiming to avoid or at least to minimize the consideration of ambiguous evolutionary events such as insertions/deletions and recurrence, which cause well-known alignment problems, in the present study we only work with the protein coding sequence, the clearly more stable region in human mitochondrial genomes. This method was tested in a small set of 99 human mtDNA comprising representatives of all major haplogroups. The developed approach showed to be a choice to automate the clustering of human mtDNA sequences into broad groups, the output being in agreement with the canonical classification into macro-haplogroups deposited in the Phylotree database. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding regionMitochondrial DNAGenome comparisonSequence alignmentProtein coding regionHaplogroup assignmentDawson constructionIn the present paper, our main goal is focused in developing fast algorithms for human mtDNA sequence analyses, requiring minimum and explicit assumptions on mutation models and evolutionary pathways. We propose a new approach based on a construction of Dawson, a technique based on the ordering of the variable sites. In this approach, the first step corresponds to the computation of the order of the positions according to their capacity to separate the sequences into dichotomous groups. Aiming to avoid or at least to minimize the consideration of ambiguous evolutionary events such as insertions/deletions and recurrence, which cause well-known alignment problems, in the present study we only work with the protein coding sequence, the clearly more stable region in human mitochondrial genomes. This method was tested in a small set of 99 human mtDNA comprising representatives of all major haplogroups. The developed approach showed to be a choice to automate the clustering of human mtDNA sequences into broad groups, the output being in agreement with the canonical classification into macro-haplogroups deposited in the Phylotree database.Elsevier2020-12-31T00:00:00Z2019-09-30T00:00:00Z2019-09-30info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10773/25204eng0166-218X10.1016/j.dam.2018.12.021Soares, InêsDuarte, RuiGuedes de Oliveira, AntónioAmorim, Antónioinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-02-22T11:49:05Zoai:ria.ua.pt:10773/25204Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T02:58:35.365490Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
title |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
spellingShingle |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region Soares, Inês Mitochondrial DNA Genome comparison Sequence alignment Protein coding region Haplogroup assignment Dawson construction |
title_short |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
title_full |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
title_fullStr |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
title_full_unstemmed |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
title_sort |
A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region |
author |
Soares, Inês |
author_facet |
Soares, Inês Duarte, Rui Guedes de Oliveira, António Amorim, António |
author_role |
author |
author2 |
Duarte, Rui Guedes de Oliveira, António Amorim, António |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Soares, Inês Duarte, Rui Guedes de Oliveira, António Amorim, António |
dc.subject.por.fl_str_mv |
Mitochondrial DNA Genome comparison Sequence alignment Protein coding region Haplogroup assignment Dawson construction |
topic |
Mitochondrial DNA Genome comparison Sequence alignment Protein coding region Haplogroup assignment Dawson construction |
description |
In the present paper, our main goal is focused in developing fast algorithms for human mtDNA sequence analyses, requiring minimum and explicit assumptions on mutation models and evolutionary pathways. We propose a new approach based on a construction of Dawson, a technique based on the ordering of the variable sites. In this approach, the first step corresponds to the computation of the order of the positions according to their capacity to separate the sequences into dichotomous groups. Aiming to avoid or at least to minimize the consideration of ambiguous evolutionary events such as insertions/deletions and recurrence, which cause well-known alignment problems, in the present study we only work with the protein coding sequence, the clearly more stable region in human mitochondrial genomes. This method was tested in a small set of 99 human mtDNA comprising representatives of all major haplogroups. The developed approach showed to be a choice to automate the clustering of human mtDNA sequences into broad groups, the output being in agreement with the canonical classification into macro-haplogroups deposited in the Phylotree database. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-09-30T00:00:00Z 2019-09-30 2020-12-31T00:00:00Z |
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://hdl.handle.net/10773/25204 |
url |
http://hdl.handle.net/10773/25204 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0166-218X 10.1016/j.dam.2018.12.021 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799137640276033536 |