Question: Finding plasmids in the draft genome sequences of bacteria isolates
2
gravatar for robjohn70000
3.9 years ago by
robjohn70000120
Nigeria
robjohn70000120 wrote:

Hi all,

How can one go about finding plasmids in the draft genome sequences of novel bacteria isolates using bioinformatics approach?

Thanks


 

ADD COMMENTlink modified 3.9 years ago by sentausa630 • written 3.9 years ago by robjohn70000120
3
gravatar for sentausa
3.9 years ago by
sentausa630
France
sentausa630 wrote:

Speaking from my personal experience, usually I compare the draft genome (typically consists of contigs or scaffolds) to a closely related genome (using Mauve) and check if there are non-matched contigs or scaffolds. Then I BLAST these non-matched contigs or scaffolds at NCBI to check if they are similar to known plasmids. 

ADD COMMENTlink written 3.9 years ago by sentausa630

Thanks a lot @sentausa for the useful info.

ADD REPLYlink written 3.9 years ago by robjohn70000120

My pleasure.

ADD REPLYlink written 3.9 years ago by sentausa630
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