In order not to prevent conflict, we can change the use of $ in jQuery to some other shortcut lile $j or $jq.
This link describes how you would implement it.
http://learn.jquery.com/using-jquery-core/avoid-conflicts-other-libraries/
For quick reference, the most common case is reproduced here.
<script src="prototype.js"></script>
<script src="jquery.js"></script>
<script>
var $j = jQuery.noConflict();
// $j is now an alias to the jQuery function;
// creating the new alias is optional.
$j(document).ready(function() {
$j( "div" ).hide();
});
// The $ variable now has the prototype meaning,
// which is a shortcut for document.getElementById().
// mainDiv below is a DOM element, not a jQuery object.
window.onload = function() {
var mainDiv = $( "main" );
}
</script>
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