microbetag : building a thorough database of genome-scale KO annotations
Description
In this repository we keep internal data for the microbetag microbial co-occurrence network annotator.
microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into.
As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file.
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chem_xref.tar.gz
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The MNXref namespace
MNXref 4.0 release notes: - The third column (evidence tag for the mapping) was suppressed - The descriptions were completed - Deprecated identifiers were moved into they own table below |
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gtdb_modelseed_gems.zip
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for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions |
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gtdb_kofam_scan_per_module.tar.gz
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all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. |
| SeedSet.pkl.gz |
A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC SeedSet |
| NonSeedSet.pkl.gz |
A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC NonSeedSet |
| seeds_per_genome.pkl.gz |
A pickle file with a binary representation of the seeds per genome . Example: cpd00493 cpd00296 cpd11431 cpd00063 cpd15717 ... |
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nonseeds_per_genome.pkl.gz
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Like above for non-seeds. |
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phen_classes.zip
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A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome. |
Files
gtdb_modelseed_gems.zip
Files
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