Found some plasmids in my sequence. IS there any tool or process by which i can find whether there are any AMR genes within those sequence?

Question

[Mustafa]

I've come across plasmids in my sequence and would like to determine if there are any antimicrobial resistance (AMR) genes present. Is there a specific tool or method available for this purpose?

[Ram]

Stop using bioinformatics as a tag. Every single post on this forum is related to bioinformatics.

Answer 1

[cfos4698]

There's another related pipeline/tool that simplifies the running of AMRFinder Plus and collates results nicely: https://github.com/MDU-PHL/abritamr (publication: https://www.nature.com/articles/s41467-022-35713-4)

[Mustafa]

I downloaded it but what should i give in the command line?

[Ram]

Read the manual.

Answer 2

[Mensur Dlakic]

There is a tool and a database:

• https://github.com/ncbi/amr
• https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047
• https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/latest/

[Mustafa]

I am fairly new to this, could you give me a run down on how to do this?