This is not so trivial problem, to say the least. I would say, this is not the problem for people who tend to say "I don't know how to start". First of all, one can start from many points, it's not the most serious problem; secondly, creating people always see many points where than can start, many. And other people has nothing to do with non-trivial problems. Who knows, may be your time has not come yet…
So, any help from this forum would be just useless. But who knows? Perhaps some introductory reading on DNA modeling can move you a bit. Please see:
http://en.wikipedia.org/wiki/Bioinformatics[
^],
http://www.eolss.net/sample-chapters/c02/E6-03B-08-05.pdf[
^],
https://sites.google.com/site/printachuth/BINFTutorialV5.0CSI07.pdf?attredirects=0[
^]…
You can find more if you do some Web search.
—SA
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