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3 KEGG Custom Modules analyses
KEMET allows for custom Modules to be added alongside the manually curated ones included in the KEGG MODULES database as listed here.
KEMET Modules files (.kk
files at KEMET/KEGG_MODULES/kk_files/
) use a specific format, which is generated with few modifications from the original KEGG MODULES entries (.txt
files at KEMET/KEGG_MODULES/
).
Custom files are to be included with other .kk
files in the local KEMET folder, in KEMET/KEGG_MODULES/kk_files/
.
Any user can include other modules by generating a file with .kk
extension and other formatting specs, listed below.
As an example, module M00023 is shown and format choices are commented.
M00023_Tryptophan biosynthesis, chorismate => tryptophan
K01657, K01658, K13503, K13501, K01656, K13497
K00766, K13497
K01817, K24017, K13498, K13501
K01656, K01609, K13498, K13501
K01695, K01696, K06001, K01694
COMPLEXES_LIST
K01657+K01658, K01695+K01696, K01695+K06001
1st line (header indications - appears in the report files):
<Module_ID>
(same as file name), an underscore character (_
), <longer_module_name>
to ease in understanding the report tables.
2nd until end/extra lines:
Each line contains sequential KEGG orthologs alternatives for a single step (see example above), separated by a comma and a space (,
).
Extra lines (in case of more complex reaction relations):
-
Adding a "COMPLEXES_LIST" tag at the end of the file enables multi-genes relations informations to be coded in the file, in the following line (e.g.
K01657+K01658
for the first step of the module in the above exemple). -
Adding an "OPTIONAL_LIST" tag at the end of the file, as in M00544 includes KOs which are not mandatory for a Module step to be considered complete, but KO presence/absence is still indicated in the report files.
-
Adding two or more "/" tags before KO lists indicates different sub-modules, which count towards the completeness in a "cumulative" fashion.
i.e. if 2 of such submodules are missing 1 KO each, the Module has 2 block missing (see M00935 as a format example). -
Adding two or more "//" tags before KO lists indicates different sub-modules, which present alternative paths (with a different number of steps) towards module completeness and as such count towards completeness in an "alternative" fashion.
i.e. if 2 of such submodules are missing 1 KO each, with the first being 8 blocks long and the second 9 blocks long, the Module will ultimately be counted as a 1 block missing with 7/8 steps (see M00026 as a format example).