Algorithm for Restriction Enzyme Analysis

Bernard P. Murray, PhD bpmurray*STUFFER* at socrates.ucsf.edu
Thu Dec 31 18:47:48 EST 1998


In article <76f0rr$m9$1 at nnrp1.dejanews.com>, bioinfo at my-dejanews.com wrote:

> Hi All,
> I am in trouble. I am developing an algorithm for restriction enzyme analysis
> but it is taking too long. The reason is because there are so many degenerate
> bases in the DNA sequence and thus it takes very long to analyze for all of
> them considering the possible combiantions they make. All the more the
> recognition sequence also have degenerate bases. Is there anybody out there to
> help me optimize the algorithm? Yes, there is. So thanking in advance to all
> those who respond.
> Ravi Gupta.
> Research Scholar
> DA University, M.P., India.

Can you clarify - are you worried about degenerate bases in the
*target* sequence in the database or in the *recognition*
sequence for the enzyme?  The former would be a rather messy
thing to play with (good luck!) but for a good implementation
of the former you may want to check out TACG (now at v2);
      http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html

I've used this for relatively big sequences and its fast enough
for me.
     I hope that this helps,
          Bernard
-- 
Bernard P. Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA



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