Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly
access the genetic content of entire communities of organisms. The field of metagenomics …

The accurate classification of viral dark matter–metagenomic sequences that originate from
viruses but do not align to any reference virus sequences–is one of the major obstacles in …

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

Reference genomes are essential for metagenomic analyses and functional characterization
of the human gut microbiota. We present the Culturable Genome Reference (CGR), a …

Background Metagenomic next-generation sequencing (mNGS) has enabled the rapid,
unbiased detection and identification of microbes without pathogen-specific reagents …

Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by
which microbiome perturbation can cause a phenotypic change in the patient. The direct …

The rapid advances of high-throughput sequencing technologies dramatically prompted
metagenomic studies of microbial communities that exist at various environments …

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It
has dispersed globally with its human host, resulting in a distinct phylogeographic pattern …

With the wide application of next-generation sequencing (NGS) techniques, fast tools for
protein similarity search that scale well to large query datasets and large databases are …

Background Analysis of mixed microbial communities using metagenomic sequencing
experiments requires multiple preprocessing and analytical steps to interpret the microbial …