Provide us your own ortholog inference data. After uploading your predictions, you will be able to compare the quality of your predictions against other orthology inference efforts using several tests.
Orthology inference is most often based on molecular protein sequences. For a comparison of different orthology prediction methods, a common set of sequences must be established. Therefore, only identical proteins are mapped to each other.
To make comparisons of method easier, the orthology research community has agreed in 2009 to established a common QfO reference proteome dataset. Currently we are using the reference proteomes from 2020_04 and 2022_02 for benchmarking. The 2011 dataset can no longer be used for benchmarking, but the results of the public projects stay for reference.
All releases of the QfO Reference Proteomes are available from UniProtKB's archive FTP server. The currently recommended datasets for benchmarking are:
See the documentation section for additional instructions how to format your orthology predictions.
This service is free for all users.
If you use the orthology benchmarking service in your work, please consider citing:
Nevers Y et al., The Quest for Orthologs benchmark service in 2022 Nucleic Acids Res, 2022 (doi: 10.1093/nar/gkac330)