Restriction Enzymes in DNA Strider?

Claude Aflalo aflaloc at BGUMAIL.BGU.AC.IL
Wed Feb 5 02:34:34 EST 1997


On 4 Feb 1997, Namjin Chung wrote:

> Dear DNA Strider Users:
> 
> I use the above software for some sequence processing, and I think it's
> simple but very good software.  The only one thing I'm not satisfied with
> it is that it would not allow custom restriction by a selected set of
> REs.  While MacVector allows you to cut DNA with the enzyme set you
> currently have, it is big and key-locked.
> 
> Does anybody know how to solve this problem?  TIA.
> 
> 
> Namjin Chung, who knows little and asks a lot!
> Program in Molecular Cancer Biology
> Duke University Medical Center
> Durham, North Carolina
> 
Here is a tips collection which will answer that

To select one or a few enzymes on strider:  Hold down the option key
when selecting digest, or graphic map.  This will bring up another
menu.  At the bottom of the menu there is a choice between triple,
double, unique, or none.  Select none.  To select a specific enzyme,
click on individual enzymes in the enzyme list.  To select more than
one, hold down the aplle (command?) key while selecting the enzyme.

_____________________________________

: In article <jpcd0-1602951411250001 at macr1-4.welc.cam.ac.uk>,
: jpcd0 at mole.bio.cam.ac.uk (John Dixon) writes:
: > P.S. BTW, does anyone know if it is possible to deselect enzymes
: > when generating a full restriction map, to avoid the huge stacks of
: > four cutters above the sequence and the enormous list of tiddly
: > fragments in the site analysis below?
:
: The only way I know of doing this is to delete enzymes manually from your
: RE
: data file.  In the same way, you can add new enzymes.
:
: - I tried modifying this file when I had the original problem, using
:   the word processor that it was originally created in, and had problems
:   with Strider crashing. Do you have any hints about how to modify it?
:   e.g. What word processor/editor do you use, and what format do you
:   choose to save it in?

I have problems editing the RE library file.  I just load it into
SimpleText or Teachtext (its predecessor) and edit away. The format goes
like:-

Spe I,      a/ctagt,
Sph I,      gcatg/c,

Taq I,      t/cga,
 (etc)
%%%%%%

; comment comment comment

This could also be done in a word processor such as Word as long as you
save it in plain text (ASCII).
Niggle/Problem
The only problem arises with the fact that I want 2 RE libraries, one for
all the enzymes in the freezer and one for all those we could buy if
needed (ie the NEB one supplied.  I keep these as two files "RE library
NEB" and "RE library -20".  To use one of these erase "RE library", I
duplicate the desired file, rename that duplicate "RE library" and run
Strider.
-----------------------------



Claude Aflalo ######################## Phones: Office 972-7-6472118 ####
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