So i have been learning AE for a couple weeks now and I can create an animated DNA strand but I was wondering if it is possible to have the audio spectrum on the sides of the double helix, and if possible how?
Very possible indeed. I am assuming you want the audio spectrum to follow the DNA strand. You said this DNA strand is automated, which i am unsure how and this method will only create a static spectrum based on where you draw your mask path.
What you will need to do is create a mask path using the pen tool on a new solid layer with the audio spectrum, that follows where you want the audio spectrum to be on the DNA strand. This will create a mask. Then in your audio spectrum settings change the 'path' drop down to the name of the mask you made and it will follow where you drew the mask on the DNA strand.
If your wanting the spectrum to flow with the DNA animation(again not knowing what it does but assuming it does a helix type animation) you will have to do whats called Rotoscoping. This is time consuming as you have to create new masks almost every few frames and then the positions of the masks are keyframes and change with time therefore with your DNA animation you want to follow. There are easy tips for this such as tracking motion and setting the values of the mask points to that output at the specific time the position changes. I have never done this but here is a resource to get you started if you need it: https://helpx.adobe.com/after-effects/using/animating-shape-paths-masks.htm...