Input
Result
Virtual digest
Enzymes: 56 commercially common enzymes, recognition sites and cut offsets from REBASE. Limit: methylation sensitivity (Dam, Dcm, CpG) and star activity are not modelled; an ambiguity code in your sequence matches no site.
METHOD
How it is calculated
Each enzyme's recognition sequence is read with IUPAC codes and searched on both strands, overlapping matches included. A palindromic site is reported once. The cut is placed from REBASE's offsets for the top and bottom strands, which also gives the end type: 5′ overhang, 3′ overhang or blunt, with its length.
Cut positions follow the convention of Biopython's Bio.Restriction: the 1-based position of the first nucleotide 3′ of the top-strand cut. On a linear molecule a cut is kept only when both strand cuts fall inside it. On a circular molecule, sites that span the origin are found and coordinates wrap. Fragment lengths are the distances between consecutive top-strand cuts of the enzymes you tick.
Which calculation this page matches
Cut positions are identical to Biopython's Bio.Restriction search on 4,032 enzyme, sequence and topology combinations, and digest fragments are identical in 50 multi-enzyme runs. They also equal Nucleora's own cloning module on every enzyme it lists.
References
- Roberts RJ, Vincze T, Posfai J, Macelis D (2023) REBASE in 2023: a database for enzymes, genes and sequences. Nucleic Acids Res 51:D629-D630. doi:10.1093/nar/gkac975
- Cock PJA, Antao T, Chang JT, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422-1423. doi:10.1093/bioinformatics/btp163
WORKED EXAMPLE
A worked example, computed by this page
A 111-bp linear fragment carrying the pUC19 multiple cloning site: positions 359 to 469 of GenBank L09137.2, reverse-complemented so that it reads along the lacZα coding strand from its start codon. 11 of the 56 enzymes cut it exactly once, among them BamHI, EcoRI, HindIII, KpnI, PstI, SacI, SalI, SmaI and others.
Ticking EcoRI and HindIII, the usual pair for directional cloning into this site, cuts at positions 19, 70 and gives:
51 bp · 42 bp · 18 bp
The middle fragment is the polylinker that a directional insert replaces.
WHERE THIS RUNS
The calculation runs in your browser
The arithmetic on this page is JavaScript executing in your browser. The sequence you enter is not sent anywhere: the calculator makes no network request with it, and there is no account, upload or server-side step. You can disconnect from the network after the page has loaded and the calculator keeps working.