What Is This Plasmid? - Identify a Backbone and Find Unexplained Regions
Paste an unlabelled plasmid and get its closest classic backbone, whether it looks like a chimera of two, and every stretch that neither a known backbone nor a known feature accounts for.
🌐 Nothing you paste is logged or stored — every tool is also callable via REST & MCP, and in bulk from the batch tools
For the tube nobody labelled, the sequence a collaborator sent with no map, or the construct whose documentation left with the person who made it. Paste the sequence and this crosses two questions against each other: which curated classic backbone does it align to, and which common features can be recognized in it - then reports the regions that NEITHER accounts for. That last list is the useful part and the part no annotation tool gives you, because it is defined by subtraction: on a construct you designed, the largest unexplained region is almost always your insert, and anything else is worth opening. On a plasmid you inherited it is the fastest way to see what somebody added. The backbone match reports identity and coverage separately, and flags a possible chimera with the positions where the alignment switches reference - which for the pUC family is often an artefact of near-identical vectors rather than real recombination, and the page says so. This is an identity and triage tool; if what you want is a labelled feature map of a plasmid you already know, the plasmid annotator does that job.
Works best on a complete plasmid — a partial read will match a backbone over less of its length and inflate the unexplained regions.
Working on a whole construct rather than one identification? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the Identify Plasmid tool
- 1Paste the full plasmid sequence, raw or FASTA. A complete sequence works far better than a partial read, which will match a backbone over less of its length and inflate the unexplained regions.
- 2Read the identity verdict first: which curated backbone is closest, at what identity over what fraction of its length, and whether the alignment switches reference part-way.
- 3Then read the unexplained regions. These are stretches no known backbone and no recognized feature covers - your insert, an undocumented part, or something worth a closer look.
- 4Check the switch points if a chimera was flagged. Between two pUC-family vectors it usually means nothing; between distant backbones it is more interesting.
Frequently asked questions
What does an unexplained region actually mean?
That neither a curated backbone alignment nor a recognized common feature covers that stretch. It is a triage signal, not a defect finding, and the distinction matters: a real gene-of-interest has no curated-backbone match and no common-feature match, so it lands in this list exactly as an unwanted duplication would. The list tells you where to look, not what you found. On a construct you designed, the biggest unexplained region is usually your insert and its presence is reassuring; on one you inherited, it is the first thing to identify.
No backbone matched. Is something wrong with my plasmid?
Almost certainly not - it is a statement about the reference set, not about your plasmid. The set is around thirty classic cloning and expression vectors, and a modern lentiviral, AAV, Gateway or synthetic-biology backbone will legitimately match none of them. The full list of what was searched is shown under every result precisely so that a no-match is readable as a limit of the search rather than a finding about the sequence.
It flagged a chimera. Should I be worried?
Usually not, and the switch points tell you which case you have. Many classic vectors share long stretches - pUC19, pUC18 and pUC118 are near-identical over much of their length - so an alignment switching between two of those is often just whichever reference aligned marginally better in that window, and means nothing. A switch between distantly related backbones is more interesting. A large insert can also break an alignment into pieces and read as a chimera; if the switch points bracket one of the unexplained regions, that is what happened.
How is this different from the plasmid annotator?
Different question. The annotator labels the features of a plasmid you already know about - promoters, origins, resistance markers, tags - and that is what you want for making a map. This one is for when you do not know what the plasmid is: it identifies the backbone, checks whether it is a hybrid, and tells you which parts nothing known explains. The feature list appears here only because the unexplained regions are defined as what neither backbone nor feature covers, and you cannot judge that list without seeing what did get covered.
Why report identity and coverage separately?
Because they fail differently and averaging them hides which happened. High identity over low coverage means your sequence matches part of that backbone very well and the rest is something else - a vector carrying a big insert, or a partial read. Lower identity over full coverage means it is a derivative of that backbone, with changes throughout. The first is a construct; the second is a relative. One number could not tell them apart.
Does the orientation matter?
Only for reading coordinates. Plasmids are circular and there is no canonical start, so a sequence can legitimately align to a reference in the reverse-complement orientation and be the same plasmid. The orientation is reported so that positions you take from here line up correctly against the reference, not as a problem to fix.
Will it work on a partial sequence?
It will run, but read the result with that in mind. A partial read covers less of the reference, which lowers the coverage figure and can make an ordinary vector look like a poor match, and any part of the plasmid you did not sequence obviously cannot be explained - so short reads inflate the unexplained regions. Use a complete plasmid sequence where you have one.
Is my data stored, and can I run this from code?
The sequence is analysed server-side and nothing is persisted. plasmid_full_report is also callable from the REST API and the MCP server, along with the narrower plasmid_identify and plasmid_annotate it combines, which is how you would triage a freezer box of unlabelled sequences rather than one tube at a time.
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