Analysis of variables of varying numbers I work with amino acid sequences and I want to use a self-made model to tell me something about it, let's call it f(seq). Now I want to know the contribution of every position in the sequence onto the model. E.q. My question is what is the importance/effect of amino acid A occurring at position I in the sequence with respect to the model? 

How do I visualize something like that?

I want to use my model also on several sequences of differing lengths. Somehow this throws a monkey wrench into my plans of using a neural net...

My question is simple yet I did not find anything about it. Pointers would be appreciated. Or any comment you might have. This whole idea of mine is pretty unfinished and I don't really know yet what I want. So feel free to criticize, I will update the question accordingly.
"My question is what is the importance/effect of amino acid A occuring at position I in the sequence with respect to the model?"

I suggest Monotony and Surprise by Apostolico for the modeling of importance of words appearing at certain positions, or in certain patterns.  Beyond that, I'm not sure what you're looking for.