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PATRIC / Pathosystems Resource Integration Center

Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic analysis of bacterial pathogens. The database provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Tools and services for bacterial infectious disease research are also available.

MetaCherchant

Extracts the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The MetaCherchant algorithm was validated on simulated datasets and applied to new ”shotgun” metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several dominant resistance genes; taxonomic annotation of the context showed the species carrying the genes. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant gives researchers an opportunity to get an insight into dynamics of resistance transmission in vivo based on metagenomic data.