A major goal of metagenomic studies is to characterize the bacterial composition of an environmental sample.
MetaPhyler is a novel taxonomic classifier for metagenomic shotgun reads,
which uses phylogenetic marker genes as a taxonomic reference.
Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database)
for each combination of taxonomic rank, reference gene, and sequence length.
Our reference database includes marker genes from all complete genomes,
several draft genomes and the NCBI nr protein database.
Results on simulated metagenomic datasets demonstrate that MetaPhyler outperforms
previous tools used in this context (CARMA, MEGAN and PhymmBL).
One major and chalenging goal in metagenomics is to identify specific functional adaptations (signatures)
of microbial communities to their habitats. Here we describe a powerful analytical method - MetaPath that
can identify differentially abundant metabolic pathways in metagenomic datasets, relying on a combination
of metagenomic sequence data and prior metabolic pathway knowledge (from KEGG).
In order to facilitate identification and characterization of antibiotic resistance genes, we have
created a manually curated database (ARDB) unifying most of the publicly available resistance genes
and related information. Resistance genes are further categorized to resistance types by their
resistance profiles and sequence similarity. Each gene or type is annotated with rich information,
including resistance profile, resistance mechanism, resistance requirement, epidemiology, GO term, COG and CDD.
DNACLUST is a tool for clustering millions of short DNA sequences.
