Identification of representative species-specific genes for abundance measurements.

ABSTRACT:

Motivation

Metagenomic binning facilitates the reconstruction of genomes and identification of Metagenomic Species Pan-genomes or Metagenomic Assembled Genomes. We propose a method for identifying a set of de novo representative genes, termed signature genes, which can be used to measure the relative abundance and used as markers of each metagenomic species with high accuracy.

Results

An initial set of the 100 genes that correlate with the median gene abundance profile of the entity is selected. A variant of the coupon collector's problem was utilized to evaluate the probability of identifying a certain number of unique genes in a sample. This allows us to reject the abundance measurements of strains exhibiting a significantly skewed gene representation. A rank-based

SUBMITTER: Zachariasen T 

PROVIDER: S-EPMC10199311 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature