Q: How to iterate through an array sequentially, where the sequence is stored as another array Here's the idea: 
var alphabet = ["A","B","C","D","E","F","G","H","I","J","K"]; 
var sequence1 = ["[i]","[i+2]","[i+2]","[i+1]","[i+4]"];

So basically I want to iterate through 'alphabet' using the sequence 'sequence1', such that the return would be: A, C, E, F, J.
I'll be having many different sequences, so it's necessary that they're each stored as their own array.

A: You can store the sequence as integers and then iterate through alphabet such as this:
var alphabet  = ["A", "B", "C", ...];
var sequence1 = [0, 2, 2, 1, 4];

for (var i = 0; i < sequence1.length; i++) {
   alphabet[sequence1[i]+i];
}

Note that, for eventual output to be A, C, E, F, J. The sequence should be 0, 1, 2, 2, 3 because arrays starts at index 0, not index 1.

A: You seem to be using sequence1 to describe how to jump from one term in the output sequence to the next, so try something like this:
var alphabet = ["A","B","C","D","E","F","G","H","I","J","K"],
    sequence1 = [0,2,2,1,4],
    pos = 0,
    newSeq = [];

for (var i = 0, l = sequence1.length; i < l; i++) {
    pos += sequence1[i];

    if (alphabet[pos] !== undefined) {newSeq.push(alphabet[pos]);}
}

which will produce an array newSeq that should be what you want.
demo: http://jsfiddle.net/BYossarian/uSmg5/
