Unknown Plasmid — What Is It and What Do I Plate On?
Which antibiotic, which host, which backbone, and what will bite you later.
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Every lab has a tube from someone who left. This reads a plasmid and answers the questions you actually have about it rather than returning another feature list: which antibiotic to plate on, which host will carry it and at roughly what copy number, which curated backbone it most resembles, and what is on it that causes trouble later — two copies of the same marker, two origins for one host, long direct repeats a recA-proficient strain can recombine out. Paste your own annotated record and it reads those annotations; paste bare bases and it runs the built-in signature scan. Either way every empty answer travels with the vocabulary it was decided against, because "nothing matched" and "nothing is there" are different statements.
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How to use the Identify an Unknown Plasmid tool
- 1Paste the plasmid — a GenBank record if you have one, otherwise bare bases.
- 2Read the plate-it-on and grows-in lines first; those are the answer.
- 3Check anything flagged below, and the coverage note before concluding something is absent.
Frequently asked questions
It says no selection marker. Does that mean the plasmid has none?
No, and the page is careful never to say so. The built-in scan knows a small number of marker families; an empty list means none of those matched. plasmid_deep_annotate searches a far larger library and is what to run before concluding a marker is absent.
Why are internal Type IIS sites not flagged as a problem?
Because nearly every plasmid has some — 4,000 bases of random sequence carry a couple by chance. They are reported as a count, and only become a flagged hazard for an enzyme you say you intend to assemble with. A warning that fires on every input teaches people to skip the warnings.
What counts as a duplicate origin?
Two origins that replicate in the SAME host. An f1 origin beside a ColE1 one is not flagged: f1 is single-strand rescue, not replication, and counting it would put a warning on every pBluescript-family vector.
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