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Identifying single copy orthologs in metazoa
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| Veröffentlicht in: | PLoS Computational Biology 7(2011,12) Artikelummer e1002269, 12 Seiten |
|---|---|
| Personen und Körperschaften: | , , |
| Titel: | Identifying single copy orthologs in metazoa/ Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork |
| Format: | E-Book-Kapitel |
| Sprache: | Englisch |
| veröffentlicht: |
December 1, 2011
|
| Gesamtaufnahme: |
Public Library of Science: PLoS Computational Biology, 7(2011,12) Artikelummer e1002269, 12 Seiten
, volume:7 |
| Schlagwörter: | |
| Quelle: | Verbunddaten SWB Lizenzfreie Online-Ressourcen |
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| 245 | 1 | 0 | |a Identifying single copy orthologs in metazoa |c Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork |
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| 520 | |a Author Summary The correct identification of single copy (1-to-1) orthologs is crucial for functional classification of genes and for phylogenetic studies of groups of organisms, including the Metazoa. Nevertheless, despite the recent increase in the number of genomes and short sequence read datasets (e.g. ESTs) from the Metazoa, we know little about their completeness and how useful they may be for phylogenetic studies. Here we describe a novel approach for the identification of single copy gene families at any hierarchical level and demonstrate its effectiveness by identifying a set of over one thousand gene families that have been in single copy since the last common ancestor of the Metazoa. By comparing our orthologs to those predicted by other datasets we show that our procedure identifies a significantly larger set of single copy orthologs in the Metazoa. We then use this dataset to assess 24 metazoan genomes and 61 metazoan EST datasets for their completeness. We thus identify the underlying error rate in genome annotation and suggest a mechanism for assessing the quality of genomes and EST datasets in terms of their suitability for phylogenetic studies. | ||
| 650 | 4 | |a Comparative genomics | |
| 650 | 4 | |a Genome annotation | |
| 650 | 4 | |a Genomic databases | |
| 650 | 4 | |a Multiple alignment calculation | |
| 650 | 4 | |a Phylogenetic analysis | |
| 650 | 4 | |a Phylogenetics | |
| 650 | 4 | |a Sequence alignment | |
| 650 | 4 | |a Sequence databases | |
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| contents | Author Summary The correct identification of single copy (1-to-1) orthologs is crucial for functional classification of genes and for phylogenetic studies of groups of organisms, including the Metazoa. Nevertheless, despite the recent increase in the number of genomes and short sequence read datasets (e.g. ESTs) from the Metazoa, we know little about their completeness and how useful they may be for phylogenetic studies. Here we describe a novel approach for the identification of single copy gene families at any hierarchical level and demonstrate its effectiveness by identifying a set of over one thousand gene families that have been in single copy since the last common ancestor of the Metazoa. By comparing our orthologs to those predicted by other datasets we show that our procedure identifies a significantly larger set of single copy orthologs in the Metazoa. We then use this dataset to assess 24 metazoan genomes and 61 metazoan EST datasets for their completeness. We thus identify the underlying error rate in genome annotation and suggest a mechanism for assessing the quality of genomes and EST datasets in terms of their suitability for phylogenetic studies. |
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| spelling | Creevey, Christopher J. VerfasserIn (DE-588)1132253268 (DE-627)887660819 (DE-576)488740592 aut, Identifying single copy orthologs in metazoa Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork, December 1, 2011, 12, Text txt rdacontent, Computermedien c rdamedia, Online-Ressource cr rdacarrier, Gesehen am 18.05.2017, Author Summary The correct identification of single copy (1-to-1) orthologs is crucial for functional classification of genes and for phylogenetic studies of groups of organisms, including the Metazoa. Nevertheless, despite the recent increase in the number of genomes and short sequence read datasets (e.g. ESTs) from the Metazoa, we know little about their completeness and how useful they may be for phylogenetic studies. Here we describe a novel approach for the identification of single copy gene families at any hierarchical level and demonstrate its effectiveness by identifying a set of over one thousand gene families that have been in single copy since the last common ancestor of the Metazoa. By comparing our orthologs to those predicted by other datasets we show that our procedure identifies a significantly larger set of single copy orthologs in the Metazoa. We then use this dataset to assess 24 metazoan genomes and 61 metazoan EST datasets for their completeness. We thus identify the underlying error rate in genome annotation and suggest a mechanism for assessing the quality of genomes and EST datasets in terms of their suitability for phylogenetic studies., Comparative genomics, Genome annotation, Genomic databases, Multiple alignment calculation, Phylogenetic analysis, Phylogenetics, Sequence alignment, Sequence databases, Arendt, Detlev VerfasserIn (DE-588)113136189X (DE-627)88602952X (DE-576)180450417 aut, Bork, Peer 1963- VerfasserIn (DE-588)122539117 (DE-627)705944476 (DE-576)293313946 aut, Enthalten in Public Library of Science PLoS Computational Biology San Francisco, Calif. : Public Library of Science, 2005 7(2011,12) Artikelummer e1002269, 12 Seiten Online-Ressource (DE-627)491436017 (DE-600)2193340-6 (DE-576)273890492 1553-7358 nnns, volume:7 year:2011 number:12 extent:12, http://dx.doi.org/10.1371/journal.pcbi.1002269 Verlag Resolving-System kostenfrei Volltext, http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002269 Verlag kostenfrei Volltext, http://dx.doi.org/10.1371/journal.pcbi.1002269 LFER, LFER 2017-06-08T00:00:00Z |
| spellingShingle | Creevey, Christopher J., Arendt, Detlev, Bork, Peer, Identifying single copy orthologs in metazoa, Author Summary The correct identification of single copy (1-to-1) orthologs is crucial for functional classification of genes and for phylogenetic studies of groups of organisms, including the Metazoa. Nevertheless, despite the recent increase in the number of genomes and short sequence read datasets (e.g. ESTs) from the Metazoa, we know little about their completeness and how useful they may be for phylogenetic studies. Here we describe a novel approach for the identification of single copy gene families at any hierarchical level and demonstrate its effectiveness by identifying a set of over one thousand gene families that have been in single copy since the last common ancestor of the Metazoa. By comparing our orthologs to those predicted by other datasets we show that our procedure identifies a significantly larger set of single copy orthologs in the Metazoa. We then use this dataset to assess 24 metazoan genomes and 61 metazoan EST datasets for their completeness. We thus identify the underlying error rate in genome annotation and suggest a mechanism for assessing the quality of genomes and EST datasets in terms of their suitability for phylogenetic studies., Comparative genomics, Genome annotation, Genomic databases, Multiple alignment calculation, Phylogenetic analysis, Phylogenetics, Sequence alignment, Sequence databases |
| swb_id_str | 488741300 |
| title | Identifying single copy orthologs in metazoa |
| title_auth | Identifying single copy orthologs in metazoa |
| title_full | Identifying single copy orthologs in metazoa Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork |
| title_fullStr | Identifying single copy orthologs in metazoa Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork |
| title_full_unstemmed | Identifying single copy orthologs in metazoa Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork |
| title_in_hierarchy | Identifying single copy orthologs in metazoa / Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork, |
| title_short | Identifying single copy orthologs in metazoa |
| title_sort | identifying single copy orthologs in metazoa |
| topic | Comparative genomics, Genome annotation, Genomic databases, Multiple alignment calculation, Phylogenetic analysis, Phylogenetics, Sequence alignment, Sequence databases |
| topic_facet | Comparative genomics, Genome annotation, Genomic databases, Multiple alignment calculation, Phylogenetic analysis, Phylogenetics, Sequence alignment, Sequence databases |
| url | http://dx.doi.org/10.1371/journal.pcbi.1002269, http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002269 |