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I've seen a few older threads on this, but no real consensus yet. Anyone have a script or method for finding circular DNAs (*osmids, minicircles) in an assembly? I suppose it's really just as "simple" as discovering the motif which is repeated and the beginning and end of the contig where it's circularized. Anyone attempted anything like this yet?
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I looked for plasmids in my assemblies by looking for contigs with the same sequence at both ends. I was able to verify that some of the contigs were plasmids by PCR and sequencing but I was not able to get a product for most of them though I was not very exhaustive in the primers that I tried. While this method works, I don't know that I would trust that you found circular DNA without a second verification.
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