New developments for the Quest for Orthologs benchmark service
The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengt...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Oxford University Press
2024
|
| _version_ | 1824458657651228672 |
|---|---|
| author | Altenhoff, A Nevers, Y Tran, V Jyothi, D Martin, M Cosentino, S Majidian, S Marcet-Houben, M Fuentes-Palacios, D Persson, E Walsh, T Lecompte, O Gabaldón, T Kelly, S Hu, Y Iwasaki, W Capella-Gutierrez, S Dessimoz, C Thomas, P Ebersberger, I Sonnhammer, E |
| author_facet | Altenhoff, A Nevers, Y Tran, V Jyothi, D Martin, M Cosentino, S Majidian, S Marcet-Houben, M Fuentes-Palacios, D Persson, E Walsh, T Lecompte, O Gabaldón, T Kelly, S Hu, Y Iwasaki, W Capella-Gutierrez, S Dessimoz, C Thomas, P Ebersberger, I Sonnhammer, E |
| author_sort | Altenhoff, A |
| collection | OXFORD |
| description | The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose. |
| first_indexed | 2025-02-19T04:29:23Z |
| format | Journal article |
| id | oxford-uuid:1049e6ed-ea58-4a50-b7a3-bc3cc1df2a0d |
| institution | University of Oxford |
| language | English |
| last_indexed | 2025-02-19T04:29:23Z |
| publishDate | 2024 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:1049e6ed-ea58-4a50-b7a3-bc3cc1df2a0d2024-12-20T20:03:42ZNew developments for the Quest for Orthologs benchmark serviceJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:1049e6ed-ea58-4a50-b7a3-bc3cc1df2a0dEnglishJisc Publications RouterOxford University Press2024Altenhoff, ANevers, YTran, VJyothi, DMartin, MCosentino, SMajidian, SMarcet-Houben, MFuentes-Palacios, DPersson, EWalsh, TLecompte, OGabaldón, TKelly, SHu, YIwasaki, WCapella-Gutierrez, SDessimoz, CThomas, PEbersberger, ISonnhammer, EThe Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose. |
| spellingShingle | Altenhoff, A Nevers, Y Tran, V Jyothi, D Martin, M Cosentino, S Majidian, S Marcet-Houben, M Fuentes-Palacios, D Persson, E Walsh, T Lecompte, O Gabaldón, T Kelly, S Hu, Y Iwasaki, W Capella-Gutierrez, S Dessimoz, C Thomas, P Ebersberger, I Sonnhammer, E New developments for the Quest for Orthologs benchmark service |
| title | New developments for the Quest for Orthologs benchmark service |
| title_full | New developments for the Quest for Orthologs benchmark service |
| title_fullStr | New developments for the Quest for Orthologs benchmark service |
| title_full_unstemmed | New developments for the Quest for Orthologs benchmark service |
| title_short | New developments for the Quest for Orthologs benchmark service |
| title_sort | new developments for the quest for orthologs benchmark service |
| work_keys_str_mv | AT altenhoffa newdevelopmentsforthequestfororthologsbenchmarkservice AT neversy newdevelopmentsforthequestfororthologsbenchmarkservice AT tranv newdevelopmentsforthequestfororthologsbenchmarkservice AT jyothid newdevelopmentsforthequestfororthologsbenchmarkservice AT martinm newdevelopmentsforthequestfororthologsbenchmarkservice AT cosentinos newdevelopmentsforthequestfororthologsbenchmarkservice AT majidians newdevelopmentsforthequestfororthologsbenchmarkservice AT marcethoubenm newdevelopmentsforthequestfororthologsbenchmarkservice AT fuentespalaciosd newdevelopmentsforthequestfororthologsbenchmarkservice AT perssone newdevelopmentsforthequestfororthologsbenchmarkservice AT walsht newdevelopmentsforthequestfororthologsbenchmarkservice AT lecompteo newdevelopmentsforthequestfororthologsbenchmarkservice AT gabaldont newdevelopmentsforthequestfororthologsbenchmarkservice AT kellys newdevelopmentsforthequestfororthologsbenchmarkservice AT huy newdevelopmentsforthequestfororthologsbenchmarkservice AT iwasakiw newdevelopmentsforthequestfororthologsbenchmarkservice AT capellagutierrezs newdevelopmentsforthequestfororthologsbenchmarkservice AT dessimozc newdevelopmentsforthequestfororthologsbenchmarkservice AT thomasp newdevelopmentsforthequestfororthologsbenchmarkservice AT ebersbergeri newdevelopmentsforthequestfororthologsbenchmarkservice AT sonnhammere newdevelopmentsforthequestfororthologsbenchmarkservice |