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Frameshift Calculator

Work out whether a deletion or insertion in a coding sequence is in frame or a frameshift, and translate the edited sequence to see where the protein changes or ends.

Formula

Δ=ninserted−ndeleted\Delta = n_{\text{inserted}} - n_{\text{deleted}}
frameshift if Δ≢0(mod3)\text{frameshift if } \Delta \not\equiv 0 \pmod 3
net change\text{net change}
the number of bases added (positive) or removed (negative)
premature stop\text{premature stop}
a stop codon in the new frame, earlier than the original one

How it works

Codons are read three bases at a time, so a change that adds or removes a number of bases that is a multiple of three keeps the reading frame, altering only the amino acids at the site. Any other change shifts the frame for all the codons downstream, which usually means a run of unrelated amino acids and, soon, a premature stop codon.

Gene knockouts with CRISPR rely on this. Double-strand breaks are repaired by end joining, which leaves small insertions and deletions, and about two in three are expected to shift the frame. The page applies the edit you describe, translates both sequences and shows where they first differ and where the new protein stops.

Worked example

A coding sequence of 93 bases with a single-base deletion at position 30.

  1. The net change is −1, not a multiple of 3, so it is a frameshift.
  2. The proteins first differ at amino acid 11, and the new frame reaches a stop at codon 19.

A frameshift, with the protein truncated from 30 to 18 amino acids by a premature stop.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • The sequence is an mRNA-style coding sequence beginning at the ATG, with no introns.
  • Only the translated sequence is considered, not the regulation of transcription, splicing or translation.

Common mistakes

  • Assuming every frameshift inactivates a gene. Some are near the end of the coding sequence, and reinitiation or exon skipping can rescue part of a protein.
  • Assuming every in-frame edit is harmless. A missing domain or a critical residue can still abolish function.
  • Counting positions from the start of the genomic sequence instead of the coding sequence.

Related tools

DNA Translation Tool (DNA to Protein)Translate in any of six reading frames with a chosen genetic codeOpen calculatorGuide RNA (gRNA) AnalyzerLength, GC content and sequence features of a CRISPR guideOpen calculatorGenome Editing Efficiency CalculatorEditing rate from reads or clones, or from a T7E1 gelOpen calculatorORF FinderOpen reading frames in all six frames, ATG to stopOpen calculator