What does it mean when "-" or "+" join KEGG orthologs in a KEGG module definition?
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Entering edit mode
18 months ago
O.rka ▴ 390

I'm looking at KEGG Module M00377. I want to calculate how complete this module is in a query set of genes to calculate a module completion ratio [MCR] based on KEGG orthologs [KO]. The way I'm calculating the MCR is the following:

p = KOs from the ORFs in the set of interest
q = KOs in the query module
r = p & q
MCR = len(r)/len(q)

However, I noticed the "Definition" for the KEGG modules has "+" or "-" values joining KOs such as the following for M00377:

{'K00198',
 'K00297',
 'K01491',
 'K01938',
 'K05299-K15022',
 'K14138+K00197+K00194',
 'K15023'}

My questions:

1. What does the "-" or the "+" mean when joining KEGG orthologs?

2. Is this the proper way to calculate MCR?

kegg ortholog module annotation metagenomics • 370 views
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