Genomic distance under gene substitutions
Autor(a) principal: | |
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Data de Publicação: | 2011 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional do INMETRO |
Texto Completo: | http://hdl.handle.net/10926/1328 |
Resumo: | Background: The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Results: Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step. Conclusions: Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology. |
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info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenomic distance under gene substitutions20112012-01-12T15:45:07Z2012-01-12T15:45:07ZBackground: The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Results: Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step. Conclusions: Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.9 p. : il.Submitted by Jonathan Barbosa (jon_crf@hotmail.com) on 2012-01-05T13:47:12Z No. of bitstreams: 1 2011_R C S Machado.pdf: 514870 bytes, checksum: 35eb41949c5216cac13ffacd4c08d30e (MD5)Rejected by Catarina Soares(cfsoares@inmetro.gov.br), reason: on 2012-01-12T11:53:40Z (GMT)Submitted by Jonathan Barbosa (jon_crf@hotmail.com) on 2012-01-12T13:39:54Z No. of bitstreams: 1 2011_R C S Machado.pdf: 514870 bytes, checksum: 35eb41949c5216cac13ffacd4c08d30e (MD5)Approved for entry into archive by Catarina Soares(cfsoares@inmetro.gov.br) on 2012-01-12T15:45:07Z (GMT) No. of bitstreams: 1 2011_R C S Machado.pdf: 514870 bytes, checksum: 35eb41949c5216cac13ffacd4c08d30e (MD5)Made available in DSpace on 2012-01-12T15:45:07Z (GMT). No. of bitstreams: 1 2011_R C S Machado.pdf: 514870 bytes, checksum: 35eb41949c5216cac13ffacd4c08d30e (MD5) Previous issue date: 2011enghttp://hdl.handle.net/10926/1328DMD_hdl_10926/1328BRAGA, Marília D. V. et al. Genomic distance under gene substitutions. BMC Bioinformatics, v. 12, 2011.Machado, Raphael Carlos SantosBraga, Marília Dias VieiraRibeiro, Leonardo CostaStoye, Jensinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional do INMETROinstname:Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO)instacron:INMETROBraga_2011.pdfhttp://xrepo01s.inmetro.gov.br/bitstream/10926/1328/1/Braga_2011.pdfapplication/pdf514870http://xrepo01s.inmetro.gov.br/bitstream/10926/1328/1/Braga_2011.pdf35eb41949c5216cac13ffacd4c08d30eMD510926_1328_1Braga_2011.pdf.txthttp://xrepo01s.inmetro.gov.br/bitstream/10926/1328/6/Braga_2011.pdf.txttext/plain40872http://xrepo01s.inmetro.gov.br/bitstream/10926/1328/6/Braga_2011.pdf.txtf897d49d3b8f2b856f6f52115fd6c2e9MD510926_1328_62024-06-10T15:24:42Zoai:xrepo01s.inmetro.gov.br:10926/1328Repositório de Publicaçõeshttp://repositorios.inmetro.gov.br/oai/requestopendoar:2012-11-01T12:59:14Repositório Institucional do INMETRO - Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO)false |
dc.title.none.fl_str_mv |
Genomic distance under gene substitutions |
title |
Genomic distance under gene substitutions |
spellingShingle |
Genomic distance under gene substitutions Machado, Raphael Carlos Santos |
title_short |
Genomic distance under gene substitutions |
title_full |
Genomic distance under gene substitutions |
title_fullStr |
Genomic distance under gene substitutions |
title_full_unstemmed |
Genomic distance under gene substitutions |
title_sort |
Genomic distance under gene substitutions |
author |
Machado, Raphael Carlos Santos |
author_facet |
Machado, Raphael Carlos Santos Braga, Marília Dias Vieira Ribeiro, Leonardo Costa Stoye, Jens |
author_role |
author |
author2 |
Braga, Marília Dias Vieira Ribeiro, Leonardo Costa Stoye, Jens |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Machado, Raphael Carlos Santos Braga, Marília Dias Vieira Ribeiro, Leonardo Costa Stoye, Jens |
description |
Background: The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Results: Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step. Conclusions: Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology. |
publishDate |
2011 |
dc.date.issued.fl_str_mv |
2011 |
dc.date.available.fl_str_mv |
2012-01-12T15:45:07Z |
dc.date.accessioned.fl_str_mv |
2012-01-12T15:45:07Z |
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/10926/1328 DMD_hdl_10926/1328 |
dc.identifier.citation.fl_str_mv |
BRAGA, Marília D. V. et al. Genomic distance under gene substitutions. BMC Bioinformatics, v. 12, 2011. |
url |
http://hdl.handle.net/10926/1328 |
identifier_str_mv |
DMD_hdl_10926/1328 BRAGA, Marília D. V. et al. Genomic distance under gene substitutions. BMC Bioinformatics, v. 12, 2011. |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
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openAccess |
dc.format.bitstream.fl_str_mv |
application/pdf text/plain |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional do INMETRO instname:Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO) instacron:INMETRO |
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Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO) |
instacron_str |
INMETRO |
institution |
INMETRO |
reponame_str |
Repositório Institucional do INMETRO |
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Repositório Institucional do INMETRO |
repository.name.fl_str_mv |
Repositório Institucional do INMETRO - Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO) |
repository.mail.fl_str_mv |
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1801499965635166208 |