"Silent" restriction sites

Michael Benedik bchs1b at ELROY.UH.EDU
Fri Nov 8 16:19:34 EST 1991


In article <1991Nov8.155818.11334 at murdoch.acc.Virginia.EDU>, wrp at cyclops.micr.Virginia.EDU (Bill Pearson) writes:
>	I have been asked if a program is available to find "silent"
>restriction sites, that is, single base changes that can be made in a
>DNA sequence that introduce a restriction site but do not change the
>protein coding sequence.
>
>	I do not believe that such a program is available in either
>EUGENE or GCG.
>
>	Can someone refer me to one?
>
>Bill Pearson
>

GCG will search for silent restriction sites. If you use the standard
restriction mapping program MAP there is a switch SILENT you can
use with it. It will look for any potential restriction sites which
are translationally silent. Another switch is MISMATCH=N which will 
allow any number of mismatches (1 or 2 etc) and find sites that many 
bases away without regard to translation. But it sounds like you
want SILENT and not MISMATCH.

In order to use MAP /SILENT you must map only the open reading frame
because that defines the translated region for the program. In other
words, if your sequence is from 1-1000 but your protein is from 30 to
929 then you must run map on 30 to 929 to define the translational
frame. You can get information by using GENHELP MAP OPTIONS
and read about the optional switches in MAP of which SILENT is one.


	---------------------------------------------------
	 Michael Benedik
	 Department of Biochemical and Biophysical Sciences
	 University of Houston
	 INTERNET: Benedik at UH.EDU	BITNET: Benedik at UHOU




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