protein sequence --> potential restriction sites?

Frank O. Fackelmayer Frank at
Fri Sep 27 03:40:41 EST 2002

Robert Whittier wrote:
> Can anyone help me out here?
> Is there a website or freeware that allows you to input a
> protein sequence and generate a list of potential
> restriction sites?

I don´t think that would be of much value. As the genetic code is
degenerated, there is a multitude of DNA sequences that could code for a
given protein sequence. When you have software to reverse-translate your
protein sequence, you´ll see what I mean. To run a restriction site
detection program over such a reverse-translated sequence will show up
essentially all restriction enzymes _potentially_ cutting somewhere in
the sequence, but almost none of them will do in real life.

> I would like to engineer some unique
> sites into a coding sequence without altering the protein.

You´ll need the DNA sequence first. In that sequence you could look for
restriction sites as usual (e.g. using the webcutter at ). The new webcutter version
"performs degenerate digests, including the option of finding
restriction sites that can be introduced into a sequence by silent
mutagenesis ("silent cutters")", which may be exactly what you´re
looking for. But, of course, you need the DNA sequence first!

hope this helps,

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