KOfam database (HMM profiles of KEGG Orthologs): licensing and KEGG

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I am working on functional annotation workflows in Galaxy using KofamScan. Currently, the tool is available, but the KOfam database (HMM profiles of KEGG Orthologs) is not installed, so I cannot select a database when running the tool.

Could you please install the KOfam database bundle required for KofamScan (HMM3 profiles + threshold files)? This will allow me to assign KO numbers to my Prodigal protein outputs and proceed with KEGG pathway completeness and visualization.

The reference for the database is:

Thank you for your help in enabling KEGG functional analysis on our Galaxy instance.

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Welcome @Pavithra_Ramamurthy

This is a good question, so I’ll try to supplement some of the other general details we have here with a bit more for this specific tool.

In short, we cannot host the KEGG indexes on the public Galaxy servers due to the academic license associated with the data.

Details can be found at this tool’s development repository at:

Then, the index it references at:

More details and alternatives are explained in this prior topic (same underlying data, different tool around it!).

There is one more option that would involve setting up a local Galaxy server (probably the Docker version), obtaining a data license, and hosting the tool/index for your own or group’s private use. This could be worth it for bulk analysis that the web portal may be unsuitable for.

Please give this a review and let us know if it helps, or if you would like to learn more about setting up your own server for this kind of data analysis. :slight_smile: