Restriction Enzymes for AA sequence database ?

Karl-Heinz Worm karl-heinz.worm at aixrs1.hrz.uni-essen.de
Wed Nov 8 01:29:25 EST 1995


>Hello Netters,
>
>Can anybody help me with  a problem. I have recently been trying to find
>some suitable restriction enzymes to cut a hole in an amino acid sequence
>, specifically DDKEL i.e. asp-asp-lys-glu-leu. You would imagine that this
>is the sort of thing that a computer would be very good at and could do
>easily.
>I thought so too but could not find a program to do it and nor can New
>England Biolabs or Boehringer Mannheim - they both said "yes, that would
>be a good idea, wouldn't it ?" but couldn't help.
>I am currently typing all possible DNA sequences that code for these AAs
>into the Mac and searching through each one but this, as you might
>imagine, is a real pain in the ass, and I would like to do this quite a
>lot without driving myself demented.
#cut#


Fergus,

I do not know about a program that can do what you were looking for, but
the following probably can make your life a little less painfully.

Get DNAid for the Mac (available from ftp.bio.indiana edu)

Type in your sequence e.g.  DDKEL  and let the prrogram translate it into
DNA. You will get the following

GAYGAYAARGARYTN

Then let the DNAid search for restriction sites in that sequence
The Programm will return all restriction sites for any of the possible DNA
sequences of your peptide. Some other programs will do the same (I guess).


Karl


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