Finding mutations conferring antibiotic resistance

Question

[robjohn70000]

Hi All,

What bioinformatics approaches can I employ to determine antibiotic resistance in bacteria strains conferred by the 23S rRNA mutation, or any other gene generally speaking?

Thanks

[GouthamAtla]

May you should read literature and look into the methods ?

Answer 1

[dago]

This is not really what you are asking for, but maybe these tools can help you :

http://en.mediterranee-infection.com/article.php?laref=283&titre=arg-annot-

http://arpcard.mcmaster.ca/?q=CARD/blast/0

[robjohn70000]

Thanks for the info @dago. Really appreciate it!

[robjohn70000]

@Geek_y and @dago, thank you both for your suggestions.

Answer 2

[sharmilla_487]

hi @robjohn any progress so far? I have the same question as well and was wondering if you could help me

[robjohn70000]

Hi @sharmilla_487, Hope you've found a solution already and if not: What I did was download the arg-annot and CARD datasets and made a local blast database of each on my computer (linux). Then I blasted my sequences against the two databases and then applied some criteria to prune down the matched 23S rRNA outputs and look for association with antibiotic resistance.