ENOG Assignment

All PhenDB predictions are performed on the bin itself, but on the set of orthologous groups of proteins (ENOGs) in which the uploaded bin’s predicted proteins are represented. Thus, in the first step, protein-coding genes are predicted in the bins/genomes provided by the user using prodigal (v.2.6.3). This is skipped if protein sequences are provided.
All protein sequences are then annotated using the bactNOG database of EggNOG 4.5.1 (http://eggnogdb.embl.de/) in highly parallelized HMMER (v.3.1b2) queries. This allows complete annotation of proteins within a microbial genome within ~2 minutes.