Operon Designer — Assemble a Polycistron and Find What the Joins Created
Build a multi-gene operon from a promoter, coding sequences and a terminator, then scan the assembled molecule for the internal promoters, ribosome binding sites and terminators that the joins created.
Assemble a bacterial operon and scan the assembled molecule rather than the parts it was built from. Supply the coding sequences in order, optionally with a promoter, an inter-gene spacer, a terminator and a host to recode for; the tool returns the assembled sequence, an annotated GenBank file, and every consensus-matching element in the molecule with its coordinates, its strand and how far it sits from consensus. The elements that break a polycistronic construct are usually created by the join and present in no part: an internal promoter reading backwards through an upstream gene, an internal ribosome binding site producing a truncated protein, a terminator-shaped hairpin cutting the message short. What is reported is what matched — a −35 and a −10 box seventeen bases apart with one mismatch, at position 812 — not a score, and not a claim that the element transcribes; for an estimated strength, the RBS Designer's promoter and translation models carry their own accuracy statements.
Paste one or more coding sequences above to assemble an operon.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the Operon Designer tool
- 1Paste your coding sequences, one per line, optionally with a name in front of each.
- 2Add a promoter, an inter-gene spacer and a terminator if you have chosen them, and pick a host if every CDS should be recoded.
- 3Press Assemble and check. The recoding is verified to translate back to the same protein, and skipped for any gene where it would not.
- 4Read the elements found in the ASSEMBLED molecule, then download the annotated GenBank or copy the sequence into a map.
Frequently asked questions
Why scan the assembled operon rather than each part?
Because the elements this finds are very often created by the junction between two parts and exist in neither. A Shine-Dalgarno sequence spanning the end of one CDS and the start of the next spacer is invisible in both parts and perfectly real in the product.
Does finding an “internal promoter” mean my construct is broken?
It means a sequence in your construct matches the sigma-70 consensus within the mismatch budget you set. Whether it actually transcribes depends on the host, the growth condition and context this tool does not read. Treat a hit as a place to look rather than a verdict; for a strength estimate, the Promoter Calculator model on the RBS Designer page gives one, with its own accuracy caveats.
Why does it search the reverse strand?
Because a promoter pointing backwards through an upstream gene does the most damage: it makes antisense RNA and knocks down expression of everything it reads through, and it is invisible to a forward-only scan. Coordinates are always reported on the forward strand, with the strand named, so you can find the hit in your own map.
What does recoding for a host actually do?
It replaces every codon with that host's most-frequent codon for the same amino acid, then checks that the result translates back to exactly the protein that went in; where it does not, that gene is left alone and a warning says so. It is a determinate rewrite, not a yield prediction: published codon-optimisation algorithms are close to a coin flip on whether they raise or lower real expression, so treat recoding as removing rare codons rather than as an expected improvement.
Why does it not assign a translation rate to each gene?
Because a translation rate is a modelled estimate and this tool is deterministic; mixing them would let an assembly step inherit a model's error bars without saying so. The RBS Designer page has both halves, rbs_predict for a rate and the RBS library designer for a ladder of them, and both carry their published validation statistics.
What does it not check?
Expression level of anything, synthesisability of the assembled sequence (run the Synthesis Complexity tool on it), mRNA folding beyond the shape of an inverted repeat, and whether any consensus match is functional. The result's gate lists all of this explicitly rather than leaving it implied.