LCA - applies also for KEGG / SEED?

User Questions
1

Dear community,
For a functional analysis of a meta-transcriptomic dataset i was running a “DIAMOND” search against the nr protein database. The tabular results were than fed into MEGAN6 (I use version 6.6.4) for a functional analysis using the KEGG and SEED accession mappers.
My question concerns the LCA algorithm of MEGAN: I understand how the algorithm filters taxonomic assignments when looking into the taxonomy tree. Correct me if i am wrong, but theoretically, the same method could be applied to filter “blastx” (or diamond) results by including only genes / functions that fulfill the user defined LCA demands (that cross the defined thresholds).

Is this happening, or can this be switched on in MEGAN6?

Thanks you and all the best,
Dan

2

Dear Dan,

the following parameters are taken into account during functional annotation:
minScore, topPercent, maxExpected and minPercentIdentity.
Also, any match to a disabled taxon is ignored.

Then MEGAN goes down the list of matches that pass the above filters and the first classification ID encountered is used.

3

Dear Daniel, Thanks for the super fast reply!