// here i selected two same ids using jquery and prototype
respectively.
<script type="javascript">
      jQuery.noConflict();
     // for jqury selectors use jQuery instead of '$ like
     jQuery(document).ready( function(){
         jQuery("id").css('color:red');
         ...
        } );'
   // then here you can write the prototype script using '$' as
selector.
    function myFun(){
         $('id').setStyle({color:red;})
     }
</script>

You can replace $ with any other variable by indicating such before
starting the script as
    var $v =jQuery.noConflict();

    $v(document).ready( fun );

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