I am using MEGAN6 for COG analysis. I blasted a set of proteins against COG database (proteins available at NCBI COG site), the results for which were imported into MEGAN. For some proteins though there were BLAST hits with COG database but the COG results in MEGAN showed no hits example for protein “>gi|378403004|emb|CCG08120.1| Reaction center protein M chain [Rhodospirillum photometricum DSM 122]” it shows hits with COG database with the cluster “COG0316” but not in MEGAN. One reason could be that this could id is not included in the eggnog databasae. If it is indeed the case how can the database be updated ?
The eggNOG files shipped with MEGAN were generated in Oct2015. I will generate new ones within the next week or two. Also, I will add all necessary tools for updating MEGANs eggNOG representation to MEGAN UE