De novo discovery of conserved gene clusters in microbial genomes with Spacedust.

ABSTRACT: Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological processes and molecular functions presents a major bottleneck. In prokaryotes and viruses, evolution favors keeping genes participating in the same biological processes colocalized as conserved gene clusters. Conversely, conservation of gene neighborhood indicates functional association. Here we present Spacedust, a tool for systematic, de novo discovery of conserved gene clusters. To find homologous protein matches, Spacedust uses fast and sensitive structure comparison with Foldseek. Partially conserved clusters are detected using novel clustering and order conservation P values. We demonstrate Spacedust's sensitivity with an all-versus-al

SUBMITTER: Zhang R 

PROVIDER: S-EPMC12510874 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature