Restriction Site Analyzer

Map restriction enzyme recognition sites in linear or circular DNA with this free online restriction site mapper for restriction digest planning, predicted digest fragments, and downstream primer design or binding validation.

Restriction site analyzer inputs

Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. Plain-text DNA, FASTA, or GenBank text only.

Use circular topology for plasmids if sites crossing base 1 or circular digest fragments matter.

Send sequence to another tool

Send the current sequence to another Mol Biology Tools page. The sequence will open in a new tab.

References

References for restriction site mapping and digest planning: REBASE-style restriction enzyme recognition sites, degenerate recognition sequences, reverse-complement scanning, and IUPAC nucleotide ambiguity codes. Mol Biology Tools implementation code is original.

  1. Restriction-enzyme recognition-site data model: Roberts et al. (2015), REBASE restriction-modification database.
  2. Current restriction-enzyme recognition and methylation details: REBASE public restriction enzyme database.
  3. Degenerate recognition-site matching: NC-IUB/IUPAC nucleotide ambiguity recommendations.