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FDA-ARGOS / data.argosdb

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Mazumder - Search CARD db for antibiotic resistance genes #281

Closed penningtonea closed 1 year ago

penningtonea commented 1 year ago

Use CARD db to find antibiotic resistance genes for ARGOS orgs

penningtonea commented 1 year ago

The following google sheets documents encompass resistance gene data available from the CARD database. The sheet labeled "CARD Resistance Prevalence" reports genes that are considered to be antibiotic resistance determinants and the corresponding resistance drug class for a given pathogen. The Resistance Gene Identifier tool uses resistance prevalence data to predict the development of AMR in viral and bacterial pathogens based on nucleotide and amino acid sequence similarities. The sheet labeled "CARD Putative AMR Resistomes" contains the RGI tool analysis results for specific NCBI nucleotide accessions.

CARD Resistance Prevalence: https://docs.google.com/spreadsheets/d/1ECIVS4Doom376Gn9u7Pvc6g9-N6067h1vwG-cyUWnHs/edit?usp=sharing

CARD Putative AMR Resistomes: https://docs.google.com/spreadsheets/d/1OasikLEvQ2R3mNWMTf2FnEK-vUW9PTN4lVh_z2UdDV0/edit?usp=sharing