So the KEGG Automatic Annotation Server's landing page (https://www.genome.jp/kegg/kaas/) indicates that it uses bi-directional best hits (BBHs for annotating "complete" genomes, while recommending using single-directional best hits (SBHs) for annotating a limited gene set ("partial genome").
My question is: why is this the case? Does the underlying annotation algorithm know when a set of sequences it is receiving represents a "complete" genome as opposed to an "incomplete" one? From what I know of the BBH methodology, it is dataset agnostic, so I don't quite see why KAAS makes this somewhat odd recommendation.
Is there some set of guidelines for when BBHs can be used?
Your inputs would be much appreciated.