Sequence Variant Comparator — Find SNPs & Indels vs a Reference
Align a query to a reference and list substitutions, insertions and deletions with effects.
🔒 Local processing — pasted sequences are not uploaded
Find out exactly what changed between two sequences. Paste a reference (wild-type or expected) and a query (your clone or a variant); the tool aligns them and reports every substitution, insertion and deletion in HGVS g. notation, with a colored side-by-side diff. Turn on “coding sequence” to see whether each substitution is synonymous, missense or nonsense — a fast way to verify a clone or characterise a mutant.
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Provide a reference and a query sequence.
Sequences are aligned globally, then differences are called relative to the reference and written in HGVS-style g. notation. Amino-acid effects are shown per substitution when “coding sequence” is on; indels that shift the frame will change everything downstream. Verify important calls against the trace/read.
How to use the Variant Comparator tool
- 1Paste the reference sequence and the query sequence.
- 2Optionally mark it as coding and set the reading-frame start.
- 3Read the variant table (HGVS + amino-acid effect) and the colored diff.
Frequently asked questions
- What kinds of variants does it report?
- Substitutions (SNPs), insertions and deletions, each with 1-based reference coordinates and HGVS-style g. notation (e.g. g.145G>A, g.20_22del, g.30_31insATG).
- How does it decide the amino-acid effect?
- With “coding sequence” on, each substitution is mapped to its codon in the chosen reading frame and classified as synonymous, missense or nonsense. Note that insertions or deletions not divisible by three shift the frame and change everything downstream.
- How are the two sequences aligned?
- With a global (Needleman–Wunsch) alignment, so the whole query is compared end-to-end against the reference. It's best for two related sequences rather than searching a large genome.