Construct QC Linter — Check a CDS Before Cloning
Scan a coding sequence for premature stops, cryptic RBS/polyA signals, unwanted restriction sites, GC extremes and repeats.
Paste a coding DNA sequence and run a full pre-cloning sanity check. The Construct / Expression QC Linter reads your reading frame to flag premature in-frame stop codons, then scans the whole sequence for internal Shine-Dalgarno-like ribosome-binding motifs (AGGAGG), polyadenylation signals (AATAAA), homopolymer runs and simple tandem repeats, GC-content extremes over a sliding window, and internal restriction sites for the enzymes in your cloning plan. Every finding is graded by severity with its exact nucleotide position, so you can fix expression-killing problems in your insert before spending on gene synthesis or a failed ligation.
0 bp
1-based nucleotide where translation begins.
Pick the enzymes in your cloning plan — internal sites that would break the digest are flagged as errors.
Enter a coding sequence to run the QC linter.
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 Construct QC Linter tool
- 1Paste a coding DNA sequence or FASTA record and set the reading-frame start if translation does not begin at nucleotide 1.
- 2Pick the restriction enzymes in your cloning plan so internal sites that would break the digest are flagged.
- 3Review the color-coded findings — errors and warnings with nucleotide positions — then fix the construct and re-lint.
Frequently asked questions
What problems does the Construct QC Linter check for?
It flags premature in-frame stop codons that truncate the protein, internal Shine-Dalgarno / ribosome-binding motifs (AGGAGG) that can cause spurious translation initiation, polyadenylation signals (AATAAA), restriction sites for enzymes in your cloning plan that would break the digest, GC-content extremes over a sliding window, and homopolymer runs or simple tandem repeats that destabilize synthesis and sequencing.
Why does the terminal stop codon not raise an error?
The premature-stop check ignores the final codon of the reading frame, since a coding sequence is expected to end in a stop. Only in-frame stops before the end are reported as errors, because they would truncate the protein.
How do I check that my insert survives a planned digest?
Select the enzymes you intend to cut with from the enzyme list. Any recognition site found inside the sequence is reported as an error labeled "restriction site to avoid", so you can silently mutate or recode it before cloning.
Can I run this from code?
Yes — the same linter is available via the REST API and the MCP server.
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