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Finding plasmids in the draft genome sequences of bacteria isolates

Hi all,

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

Thanks

next-gen-sequencing genome assembly
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updated by Ram Ram • written by robjohn70000 robjohn70000

1 answer

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.

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updated by Ram Ram • written by sentausa sentausa

Thanks a lot @sentausa for the useful info.

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updated by Ram Ram • written by robjohn70000 robjohn70000

My pleasure

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updated by Ram Ram • written by sentausa sentausa

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