Question: how to retrieve the antibiotics resistance genes in the plasmid sequence
0
gravatar for t4192
7 months ago by
t419220
t419220 wrote:

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.

genome • 210 views
ADD COMMENTlink modified 7 months ago by aquaq30 • written 7 months ago by t419220

Do you know what antibiotic resistance is expected to be present?

ADD REPLYlink written 7 months ago by genomax91k
1
gravatar for Mensur Dlakic
7 months ago by
Mensur Dlakic6.9k
USA
Mensur Dlakic6.9k wrote:

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).

ADD COMMENTlink modified 7 months ago • written 7 months ago by Mensur Dlakic6.9k
0
gravatar for aquaq
7 months ago by
aquaq30
aquaq30 wrote:

What about using CARD? https://card.mcmaster.ca/

You can either BLAST against the database or use their Resistance gene identifier (Analyze menu).

ADD COMMENTlink written 7 months ago by aquaq30
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