protein sequence --> potential restriction sites?

Frank O. Fackelmayer Frank at Fackelmayer.de
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
http://www.firstmarket.com/cutter/cut2.html ). 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,
Frank



More information about the Methods mailing list