Restriction Map

1How to use it

1. Paste the sequence. Plain or FASTA; numbers, spaces and headers are stripped, and letters keep their positions so the numbers match your own.
2. Say whether to read it as linear or circular. A plasmid is circular, and a site lying across the join is invisible in the linear reading — which turns a single cutter into a double cutter and recommends the wrong enzyme.
3. The enzymes that cut exactly once are at the top, with the position of the cut. That is the list cloning needs.
4. The table under it has every enzyme that cuts at all, fewest cuts first, with the ends it leaves and a strip showing where along the sequence the cuts fall.
5. The fold at the bottom lists the enzymes with no site here, which is the other half of the same question — an enzyme that does not cut the insert is an enzyme you can use on the vector.

2What to know

• The enzymes come from one page published by New England Biolabs, read on the date printed under the table, and nothing was added from anywhere else. 167 of the 238 specificities on it are here; the other 71 cut at a distance from their recognition site, which a site map cannot place without also modelling how far and in which direction they reach.
• ⚠️ This finds recognition sites. Whether an enzyme actually cuts one in your hands is a separate question that depends on the buffer, the temperature and how the DNA was prepared.
• Degenerate codes in a site are handled — AccI is GT/MKAC and StyI is C/CWWGG — so a degenerate site gives a degenerate overhang, printed as it is rather than resolved to one guess.
• Sticky and blunt ends are worked out from the cut position rather than looked up: the bottom strand is cut the same distance from the other end, so the overhang is what is left over. EcoRI leaves four bases 5′, KpnI four bases 3′, SmaI none.
• ⚠️ A letter that is not A, C, G or T matches nothing, including a site's own N. A site's N means any base; a sequence's N means the base is unknown, and a site nobody can confirm is not a site. Those letters keep their positions rather than being dropped, because dropping one would shift every position after it.
• One strand is searched, and that is complete rather than a shortcut: every site in this list reads the same on both strands, which is checked for all 167 rather than assumed.

3FAQs

4The other sequence tools

• DNA Reverse Complement — Reverse, complement, or reverse-complement a nucleotide sequence.
• Primer Dimer Check — Self and cross dimers, with the 3′ end called out.
• DNA to Protein Translation — Six-frame translation and open reading frames, in any NCBI genetic code.