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Data mining for proteins characteristic of clades

A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of...

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Detalles Bibliográficos
Autores principales: Bern, Marshall, Goldberg, David, Lyashenko, Eugenia
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636346/
https://www.ncbi.nlm.nih.gov/pubmed/16936320
http://dx.doi.org/10.1093/nar/gkl440
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author Bern, Marshall
Goldberg, David
Lyashenko, Eugenia
author_facet Bern, Marshall
Goldberg, David
Lyashenko, Eugenia
author_sort Bern, Marshall
collection PubMed
description A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and γ-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools.
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spelling pubmed-16363462006-11-29 Data mining for proteins characteristic of clades Bern, Marshall Goldberg, David Lyashenko, Eugenia Nucleic Acids Res Computational Biology A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and γ-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools. Oxford University Press 2006-09 2006-08-26 /pmc/articles/PMC1636346/ /pubmed/16936320 http://dx.doi.org/10.1093/nar/gkl440 Text en © 2006 The Author(s)
spellingShingle Computational Biology
Bern, Marshall
Goldberg, David
Lyashenko, Eugenia
Data mining for proteins characteristic of clades
title Data mining for proteins characteristic of clades
title_full Data mining for proteins characteristic of clades
title_fullStr Data mining for proteins characteristic of clades
title_full_unstemmed Data mining for proteins characteristic of clades
title_short Data mining for proteins characteristic of clades
title_sort data mining for proteins characteristic of clades
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636346/
https://www.ncbi.nlm.nih.gov/pubmed/16936320
http://dx.doi.org/10.1093/nar/gkl440
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