Question: Identify a sequence as plasmid
gravatar for utkarsh.sood
4.5 years ago by
utkarsh.sood30 wrote:


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 sequence genome • 2.0k views
ADD COMMENTlink modified 4.5 years ago by sentausa640 • written 4.5 years ago by utkarsh.sood30

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.

ADD REPLYlink written 4.5 years ago by harold.smith.tarheel4.5k

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.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Martombo2.6k
gravatar for sentausa
4.5 years ago by
sentausa640 wrote:

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.

ADD COMMENTlink written 4.5 years ago by sentausa640
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