Identify a sequence as plasmid
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6.1 years ago
utkarsh.sood ▴ 40

Hello

I have a 61 kb sequence generated during the sequencing of whole genome of a bacteria. The main chromosome is 6.2Mb and have all the essential copy genes whereas the 61 Kb sequence does not have any chromosomal genes. What should I do to show that this sequence is of the plasmid. 

 

myposts genome sequence • 2.5k views
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A plasmid will be circular, so you would have reads that contain both end sequences (3' followed by 5'). Higher than average copy number is another clue, but repeat elements (e.g., multiple insertions of a transposon or prophage) will also share this characteristic.

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do you expect the plasmid to be present in multiple copies? if so, also the sequencing coverage should be higher. this could be an indication of an actual plasmid.

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6.1 years ago
sentausa ▴ 640

Did you BLAST it on Genbank? Or, if you already know related bacteria which have available sequenced plasmids, you might try to align it against these plasmids.

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