MKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data.

ABSTRACT: The advanced single-microbe RNA sequencing (smRNA-seq) technique addresses the pressing need to understand the complexity and diversity of microbial communities, as well as the distinct microbial states defined by different gene expression profiles. Current analyses of smRNA-seq data heavily rely on the integrity of reference genomes within the queried microbiota. However, establishing a comprehensive collection of microbial reference genomes or gene sets remains a significant challenge for most real-world microbial ecosystems. Here, we developed an unbiased embedding algorithm utilizing K-mer signatures, named mKmer, which bypasses gene or genome alignment to enable species identification for individual microbes and downstream functional enrichment analysis. By substituting gene features

SUBMITTER: Mo F 

PROVIDER: S-EPMC12100620 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature