use strict;
use warnings;

my $s = do {local $/=undef; <DATA>};
use XML::Simple;
my $data = XMLin("<opt>$s</opt>", KeepRoot => 0);
#use Data::Dumper;
#print Dumper $data;

my $search_string = "dog cat cow";  # from input
my %searchwords = map { $_ => undef } split ' ', $search_string;
while( my ($k, $h) = each %$data ){
  my $score = scalar grep( exists $searchwords{$_}, split(/, /, $h->{words}) );
  # do whatever based on score.
}

__DATA__
<MS_1>
  <loc>c:\data\cat.xml</loc>
  <words>dog, cat, fish, bird</words>
</MS_1>

<MS_2>
  <loc>c:\data\cow.xml</loc>
  <words>dog, cat, fish, bird, cow, goat</words>
</MS_2>

<MS_3>
  <loc>c:\data\snake.xml</loc>
   <words>dog, cat, fish, bird, snake, orange</words>
</MS_3>