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2 KEMET use of KEGG annotations

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Matteopaluh edited this page Jan 10, 2023 · 1 revision

Examples of KEGG annotations

The files cited in this wiki page (and present in the KEMET/toy folder) are examples of input KEGG annotations.
This page includes a discussion about the different formats, along with info on how to use the different output files within KEMET. Said files only include the first few lines of what an actual functional annotation file would be made of, only to show their formatting differences.

The files extension does not need to be modified, neither the rest of file name, except it does not refer to the same genome in input (e.g. the toy files included here are meant to be used only with a genome called bin1.fasta, bin1.fa or bin1.fna).

To use annotations files, these need to be copied in the KEMET/KEGG_annotations/ folder, created in the setup process.

  • bin1.emapper.annotations is an example of one of the files that can be generated using either eggNOG mapper command line program or the web server (other files, e.g. in this case bin1.seed_orthologs, are NOT used by KEMET and should NOT be included in the annotation folder).
    To use this type of annotation within kemet.py script, the user will need to add the -a or --annotation_format argument, then write "eggnog": -a eggnog

  • bin1.ko is an example of a file generated via KAAS (KEGG Automatic Annotation Server), which can be accessed here.
    To utilize this type of annotation within kemet.py script, the user will need to add the -a or --annotation_format argument, then write "kaas": -a kaas

  • bin1_ko.txt is an example of a KofamKOALA output obtained via command line (Kofamscan - mapper format) or via web server, if downloaded with the "Input file for KEGG Mapper" option. This file has the same format of those generated via KAAS, i.e. a tabular file with two fields, one indicating a gene-id, the other either being empty or indicating either a KEGG Ortholog (KO). Within the KEMET vocabulary, this is referred to as "kaas-like". To utilize this type of annotation within kemet.py script, the user will need to add the -a or --annotation_format argument, then write "kaas": -a kaas

  • bin1.txt and bin1.tsv are examples of files generated via KofamKOALA, which is accessed either via command line (Kofamscan - detail or detail-tsv format) or via web server. Specifically, if the request is executed via web server, this file is the output that can be downloaded with the "result file" option.
    To utilize this type of annotation within kemet.py script, the user will need to add the -a or --annotation_format argument, then write "kofamkoala": -a kofamkoala

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