How Could I Do This...

I want to make a game where you are in a science lab and in the first round you must pick certain things to do in a order to test DNA. Then there would be a different round. In that round you have a big long strand of DNA code. (Example... ATCGCGTAATGCGTAGTCATGCACAT) Then you get a certain amount of points for a certain sequence like ATCG. When you find it you mark it with a little radioactive marker. You get 3 markers to try to get a certain amount of points. If you get that amount of points you test the DNA again and try round two with a different long strand of DNA.

This is a pretty compicated game and I'm not sure where to even start. Have any code, advice or ways to do it? PLEASE POST!!! Your help is greatly needed!

----SOON I WILL POST THE URL OF MY DNA WEBSITE. (I STILL HAVE TO PUT IT ON THE WEB.) MANY OF YOU HAVE HELPED MAKE IT PRETTY GOOD SO FAR.----