Finding plasmids in the draft genome sequences of bacteria isolates

Question

[robjohn70000]

Hi all,

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

Thanks

Answer 1

[sentausa]

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.

[robjohn70000]

Thanks a lot @sentausa for the useful info.

[sentausa]

My pleasure