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We implemented a bioinformatics workflow (Agnostos) to structure and explore the large pool of genes with unknown functions found in microbial genomes and metagenomes. We used a protein domain-based approach to partition more than 400 million predicted genes from 1,628 metagenomes and ~29 genomes into different categories of gene clusters of known and unknown functions.

Agnostos workflow different modules

The AGNOSTOS WORKFLOW can be found HERE.

The methods (included all the scripts/code) and results for each module are documented. Below you can find the links to the different reports:

DATA

Workflow steps

• 1. Gene prediction

• 2. MMseqs clustering

• 3. Pfam annotations

• 4. Cluster validation

• 5. Cluster refinement

• 6. Cluster classification in categories

• 7. Known-Unknown cluster category refinement

• 8. Cluster communities inference

Main analyses and results:

• Cluster and communities overview

• Coverage of external databases

• EUs in MAGs

• GTDB genomes integration

• Environmental analyses

• Phylogenomic analyses

• TARA ocean OM-RGC-v.2 integration

• Mutant phenotypes

• Results in numbers