Microbial 'omics


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kegg-data [artifact]

Table of Contents

DB

A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

🔙 To the main page of anvi’o programs and artifacts.

Provided by

anvi-setup-kegg-kofams

Required or used by

anvi-display-metabolism anvi-estimate-metabolism anvi-run-kegg-kofams

Description

A directory of data downloaded from the KEGG database resource for use in function annotation and metabolism estimation.

It is created by running the program anvi-setup-kegg-kofams. Not everything from KEGG is included in this directory, only the information relevant to downstream programs. The most critical components of this directory are KOfam HMM profiles and the modules-db which contains information on metabolic pathways as described in the KEGG MODULES resource.

Programs that rely on this data directory include anvi-run-kegg-kofams and anvi-estimate-metabolism.

Directory Location

The default location of this data is in the anvi’o folder, at anvio/anvio/data/misc/KEGG/.

You can change this location when you run anvi-setup-kegg-kofams by providing a different path to the --kegg-data-dir parameter:

anvi-setup-kegg-kofams --kegg-data-dir /path/to/directory/KEGG

If you do this, you will need to provide this path to downstream programs that require this data as well.

Directory Contents

Here is a schematic of how the kegg-data folder will look after setup:

KEGG
 |- MODULES.db
 |- ko_list.txt
 |- modules.keg
 |- HMMs
 |   |- Kofam.hmm
 |   |- Kofam.hmm.h3f
 |   |- (....)
 |
 |- modules
 |   |- M00001
 |   |- M00002
 |   |- (....)
 |
 |- orphan_data
     |- 01_ko_fams_with_no_threshold.txt
     |- 02_hmm_profiles_with_ko_fams_with_no_threshold.hmm

Typically, users will not have to work directly with any of these files, as downstream programs will interface directly with the modules-db.

However, for the curious: ko_list.txt, modules.keg, and all files in the modules subfolder are flat text files downloaded from the KEGG website. The data in these files are processed and organized into the modules-db for easier programmatic access.

The HMMs subfolder contains a file of concatentated KOfam profiles (also originally downloaded from KEGG), as well as the indexes for this file. Some KOfam profiles do not have a score threshold in the ko_list.txt file - these profiles and their corresponding entries from that file live in the orphan_data directory. Please note that KOs from the orphan_data directory will not be annotated in your contigs-db when you run anvi-run-kegg-kofams.

Edit this file to update this information.