Didn't @epcrocha or @martibartfast @ZaminIqbal create tools to analyze that? (sorry for tagging)
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Yes we produced probes for detecting MOBs and T4SS and scanned the SRA, using BIGSI here https://www.nature.com/articles/s41587-018-0010-1 … So, you could make a BIGSI index of your plasmids and search for these. But you might find mob-suite better:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6159552/ …
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oriT finder is a good start
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Following... Perhaps annotation and something like OriT finder... but not always conclusive so we try quick screening in vitro
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I just came across CONjscan, a HMM based tool to identify relaxase and secretion systems - https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/odoppelt/conjscan/ConjScan/1.0.2 …
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