KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

Aramaki et al. (Mon,) studied this question.

www.synapsesocial.com/papers/69d7f16211d83f35e5ae364f — DOI: https://doi.org/10.1093/bioinformatics/btz859

Also consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs· 1997 · 74,373 citations
2. CD-HIT: accelerated for clustering the next-generation sequencing data· 2012 · 11,666 citations
3. KEGG: Kyoto Encyclopedia of Genes and Genomes· 2000 · 38,891 citations
4. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences· 2015 · 4,245 citations
5. GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array· 2014 · 92 citations