Question: Finding mutations conferring antibiotic resistance
1
gravatar for robjohn70000
4.6 years ago by
robjohn70000120
Nigeria
robjohn70000120 wrote:

Hi All,

 

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

 

Thanks

sequencing blast snp gene genome • 1.3k views
ADD COMMENTlink modified 17 months ago by sharmilla_4870 • written 4.6 years ago by robjohn70000120
2

May you should read literature and look into the methods ?

ADD REPLYlink written 4.6 years ago by geek_y9.8k
0
gravatar for dago
4.6 years ago by
dago2.5k
Germany
dago2.5k wrote:

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

ADD COMMENTlink written 4.6 years ago by dago2.5k

Thanks for the info @dago. Really appreciate it!

ADD REPLYlink written 4.6 years ago by robjohn70000120

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

ADD REPLYlink written 4.6 years ago by robjohn70000120
0
gravatar for sharmilla_487
17 months ago by
sharmilla_4870 wrote:

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

ADD COMMENTlink written 17 months ago by sharmilla_4870

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.

ADD REPLYlink written 17 months ago by robjohn70000120
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