I want to annotate a new virus I am studying. I was able to annotate most of the genes with pharokka. I want to annotate the remaining 50 hypothetical/unknown proteins. I used hmmscan with PFAM and TIGRFAM databases and was able to find 10 supplementary annotations. Now I want to do the same with eggNOG but I am very confused by the results.
I downloaded bactNOG with http://eggnog45.embl.de/download/eggnog_4.5/data/bactNOG/bactNOG.hmm.tar.gz, concatenated all the hmm files in one big hmm file and used hmmpress to create the hmm database.
Then i did the hmmscan as before but the results are not usable because the target names are ENOG numbers and not protein names (see the first column of the image below):
I tried to look for these numbers on the eggNOG website but I always got "No results found" (example with ENOG41068Q0 or just the last 5 characters 068Q0). PFAM and TIGRFAM on the contrary provided information on the hits via the last column "description of target":
Does anyone have experience with eggNOG and understands the problem? I know eggNOG-mapper exists but I would like to use hmmer to have the same process for all the databases I try.
Any help would be appreciated :)
