how to retrieve the antibiotics resistance genes in the plasmid sequence
I have a nucleotide sequence of a 300kb bacterial plasmid. I want to get the antibiotics resistance genes on this plasmid. How can I get the gene list? I have the Linux command line skills. Please recommend some websites or software for me.
2 answers
A simple Google search seems to do the trick. After downloading the database(s), translate your plasmid in 6 reading frames taking only ORFs larger than 150-200 amino-acids, and BLAST them against the database(s).
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Mensur Dlakic
What about using CARD? https://card.mcmaster.ca/
You can either BLAST against the database or use their Resistance gene identifier (Analyze menu).
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Do you know what antibiotic resistance is expected to be present?