Virulence Factor Database for 16S metagenomics
Description
Virulence-relevant KOs Database allows the prediction of bacterial virulence factor genes from 16S-based metagenomics using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. After normalisation for 16S rDNA copy number and total species count, KEGG Orthologs (KO) abundances can be estimated using PICRUSt pre-computed files and virulence-specific genes parsed using VFDB_KO_unique file.
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Steps to reproduce
Virulence-relevant KOs database was constructed by mapping non-redundant VFDB (set B) nucleotide sequences GI from the Virulence Factor Database (VFDB) and accession numbers (updated according to the prokaryotic RefSeq genome re-annotation project) to Uniprot identifiers (UPI) and then to KO using BioServices tool. This resulted in 1197 unique virulence KO, among which 989 (83%) mapped to PICRUSt pre-calculated reference file. Virulence KO were categorised into virulence functions according to the VFDB classification.