New developments for the Quest for Orthologs benchmark service.

Details

Serval ID
serval:BIB_3CD5DDCF6532
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
New developments for the Quest for Orthologs benchmark service.
Journal
NAR genomics and bioinformatics
Author(s)
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.D., Ebersberger I., Sonnhammer E.
ISSN
2631-9268 (Electronic)
ISSN-L
2631-9268
Publication state
Published
Issued date
12/2024
Peer-reviewed
Oui
Volume
6
Number
4
Pages
lqae167
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
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.
Pubmed
Open Access
Yes
Create date
16/12/2024 16:49
Last modification date
17/12/2024 7:09
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