Testing your own method

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.

QfO Reference Proteomes Dataset

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 establish a common QfO reference proteome dataset. Currently, we are using the reference proteomes from 2020_04 and 2022_02 for benchmarking. The older datasets can no longer be used for benchmarking, but the results of the public projects stay for reference.

Dataset sources

All releases of the QfO Reference Proteomes are available from UniProtKB's archive FTP server. The currently recommended datasets for benchmarking are:

  • 2020_04: Allows comparisons with the most methods.
  • 2022_02: Newer version of reference dataset. This release allows comparisons with fewer methods, but contains additional new benchmarks.
Both datasets are recommended for benchmarking.

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)

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