POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.

Detalhes bibliográficos
Autor(a) principal: HONGO, J. A.
Data de Publicação: 2015
Outros Autores: CASTRO, G. M. de, CINTRA, L. C., ZERLOTINI, A., LOBO, F. P.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1027912
Resumo: Abstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection.
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spelling POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.PotionEvolução DarwinianaComparative genomicsPositive selectionGeneFenótipoPesquisaGenomicsPhylogenyGenesGenomeAbstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection.JORGE A. HONGO, Bolsista CNPTIA; GIOVANNI M. DE CASTRO, Bolsista CNPTIA; LEANDRO CARRIJO CINTRA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA.HONGO, J. A.CASTRO, G. M. deCINTRA, L. C.ZERLOTINI, A.LOBO, F. P.2015-11-04T11:11:11Z2015-11-04T11:11:11Z2015-11-0420152016-06-22T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleBMC Genomics, London, v. 16, p. 1-16, Aug. 2015.http://www.alice.cnptia.embrapa.br/alice/handle/doc/102791210.1186/s12864-015-1765-0enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-08-16T03:07:44Zoai:www.alice.cnptia.embrapa.br:doc/1027912Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542017-08-16T03:07:44falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-08-16T03:07:44Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
title POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
spellingShingle POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
HONGO, J. A.
Potion
Evolução Darwiniana
Comparative genomics
Positive selection
Gene
Fenótipo
Pesquisa
Genomics
Phylogeny
Genes
Genome
title_short POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
title_full POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
title_fullStr POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
title_full_unstemmed POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
title_sort POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.
author HONGO, J. A.
author_facet HONGO, J. A.
CASTRO, G. M. de
CINTRA, L. C.
ZERLOTINI, A.
LOBO, F. P.
author_role author
author2 CASTRO, G. M. de
CINTRA, L. C.
ZERLOTINI, A.
LOBO, F. P.
author2_role author
author
author
author
dc.contributor.none.fl_str_mv JORGE A. HONGO, Bolsista CNPTIA; GIOVANNI M. DE CASTRO, Bolsista CNPTIA; LEANDRO CARRIJO CINTRA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA.
dc.contributor.author.fl_str_mv HONGO, J. A.
CASTRO, G. M. de
CINTRA, L. C.
ZERLOTINI, A.
LOBO, F. P.
dc.subject.por.fl_str_mv Potion
Evolução Darwiniana
Comparative genomics
Positive selection
Gene
Fenótipo
Pesquisa
Genomics
Phylogeny
Genes
Genome
topic Potion
Evolução Darwiniana
Comparative genomics
Positive selection
Gene
Fenótipo
Pesquisa
Genomics
Phylogeny
Genes
Genome
description Abstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection.
publishDate 2015
dc.date.none.fl_str_mv 2015-11-04T11:11:11Z
2015-11-04T11:11:11Z
2015-11-04
2015
2016-06-22T11:11:11Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv BMC Genomics, London, v. 16, p. 1-16, Aug. 2015.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1027912
10.1186/s12864-015-1765-0
identifier_str_mv BMC Genomics, London, v. 16, p. 1-16, Aug. 2015.
10.1186/s12864-015-1765-0
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1027912
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 EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
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