Restriction Enzymes in DNA Strider?

Harry Mangalam mangalam at uci.edu
Tue Feb 4 17:52:21 EST 1997


In article <nc1-0402971130080001 at phanes94.mc.duke.edu>, nc1 at acpub.duke.edu
(Namjin Chung) wrote:
> 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.

You can solve this with DNA Strider by making subfiles of the enzymes that
you want and renaming them "RELibrary" as you need them, although you'll
have to restart Strider evey time you want to use another subset.  Not a
very elegant way of doing it, but it allows you to keep using the program
you're used to.

Most commercial sequence analysis apps allow you to specify subsets of
enzymes by explicit groupings, or other characteristics, such as all 5'
cutters, those that cut more or less than X times, those that recognize
only sequences more than Y bases, etc.

I've put a web interface on my *FREE* restriction enzyme analysis app
'tacg', and you can specify enzymes via overhang, magnitude of recognition
sequence, number of cuts, explicit picks, subsets via different files (ie
enzymes from different vendors, or sorted via price), etc, etc, etc. Also
works with the transcription factor database, as a quick and dirty version
of Dan Prestridge's 'signalscan'.

Output is via linear map, 1/3/6 frames of translation in 1 or 3 letter
code, pseudo-graphical ladder map and/or gel simulation, fragments (sorted
or not), cut site, etc.  It handles sequence into the millions of bases, if
you have the RAM; it was designed for scanning genome sized chunks of DNA.

   The idea was to get Strider-like output for unix systems via a
command-line program.  It just happened that it's relatively easy to port
it to the web, so I did.

YOu can get a better idea about it by peeking at the web page:

http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html

the Web form is at:

http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html

If you use Netscape, you can upload files to it as well as using paste-in;
I'm not sure about other browsers.

Cheers
Harry
-- 
Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII  UC
Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598



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