OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem
Abstract In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particula...
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| Veröffentlicht in: | Nucleic acids research 2024-01, Vol.52 (D1), p.D513-D521 |
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| creator | Altenhoff, Adrian M Warwick Vesztrocy, Alex Bernard, Charles Train, Clement-Marie Nicheperovich, Alina Prieto Baños, Silvia Julca, Irene Moi, David Nevers, Yannis Majidian, Sina Dessimoz, Christophe Glover, Natasha M |
| description | Abstract
In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
Graphical Abstract
Graphical Abstract |
| doi_str_mv | 10.1093/nar/gkad1020 |
| format | Article |
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In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
Graphical Abstract
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In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
Graphical Abstract
Graphical Abstract</description><subject>Ecosystem</subject><subject>Evolution, Molecular</subject><subject>Genome - genetics</subject><subject>Phylogeny</subject><subject>Proteome</subject><subject>Synteny</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kT1PHDEQhq0oUTggXerIXVKwwd_YdAjxJYGugXrl9c7ebdi1D9t3Yf8FPxkfBylTvaPR43c88yL0nZLflBh-7G08XjzalhJGPqEZ5YpVwij2Gc0IJ7KiROg9tJ_SH0KooFJ8RXv8pABcqhl6md-d4RDzMgxhMeHeY0aYOMX9uIphAy0u8mjjFDJgVxrRLuAIW-8g5WiHUrUYnrP1GV_NMfjYu-UIPhcGR9jYcVU80uQz-AlvevgL8e3NGCJsp-Ul4O0XLlxIU8owHqIvnR0SfHvXA_RweXF_fl3dzq9uzs9uK8cMzRXIhrFONYY0QpoTpql0THVFodO84dJRoVpBHbWUt6TVWpRWa5XUmjTS8AP0a-dbFnxal23qsU8OhsF6COtUM62NMVwpUdCjHepiSClCV69iP5aj1JTU2wzqkkH9kUHBf7w7r5sR2n_wx9EL8HMHhPXq_1avxBiQnQ</recordid><startdate>20240105</startdate><enddate>20240105</enddate><creator>Altenhoff, Adrian M</creator><creator>Warwick Vesztrocy, Alex</creator><creator>Bernard, Charles</creator><creator>Train, Clement-Marie</creator><creator>Nicheperovich, Alina</creator><creator>Prieto Baños, Silvia</creator><creator>Julca, Irene</creator><creator>Moi, David</creator><creator>Nevers, Yannis</creator><creator>Majidian, Sina</creator><creator>Dessimoz, Christophe</creator><creator>Glover, Natasha M</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-8354-5350</orcidid><orcidid>https://orcid.org/0000-0001-7492-1273</orcidid><orcidid>https://orcid.org/0000-0002-7318-9065</orcidid><orcidid>https://orcid.org/0009-0007-5042-2323</orcidid><orcidid>https://orcid.org/0000-0001-5345-6982</orcidid><orcidid>https://orcid.org/0000-0002-4074-4261</orcidid><orcidid>https://orcid.org/0000-0003-1811-4340</orcidid><orcidid>https://orcid.org/0000-0002-1332-7948</orcidid><orcidid>https://orcid.org/0000-0002-8604-2943</orcidid><orcidid>https://orcid.org/0000-0002-2664-7385</orcidid><orcidid>https://orcid.org/0000-0002-2170-853X</orcidid></search><sort><creationdate>20240105</creationdate><title>OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem</title><author>Altenhoff, Adrian M ; Warwick Vesztrocy, Alex ; Bernard, Charles ; Train, Clement-Marie ; Nicheperovich, Alina ; Prieto Baños, Silvia ; Julca, Irene ; Moi, David ; Nevers, Yannis ; Majidian, Sina ; Dessimoz, Christophe ; Glover, Natasha M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c291t-e5b22f6b90b45972815c26f281ef83b35c146d41c1a13d0d8845c1da65880b593</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Ecosystem</topic><topic>Evolution, Molecular</topic><topic>Genome - genetics</topic><topic>Phylogeny</topic><topic>Proteome</topic><topic>Synteny</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Altenhoff, Adrian M</creatorcontrib><creatorcontrib>Warwick Vesztrocy, Alex</creatorcontrib><creatorcontrib>Bernard, Charles</creatorcontrib><creatorcontrib>Train, Clement-Marie</creatorcontrib><creatorcontrib>Nicheperovich, Alina</creatorcontrib><creatorcontrib>Prieto Baños, Silvia</creatorcontrib><creatorcontrib>Julca, Irene</creatorcontrib><creatorcontrib>Moi, David</creatorcontrib><creatorcontrib>Nevers, Yannis</creatorcontrib><creatorcontrib>Majidian, Sina</creatorcontrib><creatorcontrib>Dessimoz, Christophe</creatorcontrib><creatorcontrib>Glover, Natasha M</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Altenhoff, Adrian M</au><au>Warwick Vesztrocy, Alex</au><au>Bernard, Charles</au><au>Train, Clement-Marie</au><au>Nicheperovich, Alina</au><au>Prieto Baños, Silvia</au><au>Julca, Irene</au><au>Moi, David</au><au>Nevers, Yannis</au><au>Majidian, Sina</au><au>Dessimoz, Christophe</au><au>Glover, Natasha M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2024-01-05</date><risdate>2024</risdate><volume>52</volume><issue>D1</issue><spage>D513</spage><epage>D521</epage><pages>D513-D521</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>Abstract
In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
Graphical Abstract
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| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2024-01, Vol.52 (D1), p.D513-D521 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Ecosystem Evolution, Molecular Genome - genetics Phylogeny Proteome Synteny |
| title | OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem |
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