I would use Python rather than Java for this sort of task.
In Java, however, you should only use an ArrayList over a char[] array if you will be adding/removing elements after you initially create the collection.
@Iftikhar: You miscapitalized "ToCharArray" in your code (it should be "toCharArray"). As for your enhanced for loop, the keyword is still "for", not "foreach", and the separator is a colon, not "in". Also, the add method for an ArrayList is "add", not "Add". Next time please ensure that your code compiles and runs successfully before posting.
// The original sequence as a String
String sequence = "CAENBVWGKL";
// Convert it to an array of char
char[] seqChars = sequence.toCharArray();
// Now you can easily access each character
System.out.println(seqChars[0]);
// If you want an ArrayList instead
ArrayList<Character> seqList = new ArrayList<Character>();
for (char c : seqChars)
seqList.add(c); // Add each character to the list