Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.

ABSTRACT:

Motivation

Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

Results

Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and

SUBMITTER: Kananen K 

PROVIDER: S-EPMC11964587 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature