A) tr/// isn't what you want (even if you'd used a syntactically correct trailing slash). s/// is for substitutions.

B) unless you can guarantee a very strict formatting in the HTML you're operating on you don't want to use a regexp to manipulate HTML. Use HTML::TokeParser or HTML::TreeBuilder or the like.

[ The OP silently updated his question. This post is now obsolete. ]

So, let me get this straight. You have a user-entered search phrase and you want to highlight HTML content where it matches those words.

First, let me recommend that when you change your node, you mark it as Update: and either use strike notation or simply post your updated material in a separate paragraph, leaving your original post content alone.

Second, you want to parse out a search phrase into words and put them in an array -- use split to accomplish this.

Third, you'll want to step through that array, using a construct like this (untested):

  for my $word (@search_words) {
    $html =~ s/($word)/<b><u>$1<\/u><\/b>/g;
  }
[download]

This acts on the HTML in $html that you are evaluating and replaces $word with a highlighted version of itself (that's what the $1 accomplishes). It acts on the entire contents of $html because of the /g modifier on the regex.

Fourth, if you want to parse out sections or tags of HTML, applying your substitution to some while ignoring others, you'll probably want to use a CPAN module to do that. I've used HTML::TreeBuilder for such things before, but you may want to search around a little for something that suits your needs.

Update: Ah, I see that Fletch already recommended this. Well, now you've heard it from two people! :)

use strict;
use HTML::TokeParser::Simple;
use Getopt::Std;

my $Usage = "Usage: $0 -f word file.html > highlighted.html\n";

my %opts;
( getopts( 'f:', \%opts ) and $opts{f} and @ARGV == 1 )
    or die $Usage;

$opts{f} =~ tr/,/\|/;

# This applies a regex substitution to the text part
# and leaves the tags unmodified:

while ( my $token = $p->get_token ) {
    if ( $token->is_text ) {
        $_ = $token->as_is;
        s{($opts{$f})}{<b><u>$1</u></b>}g;
        print;
    }
    else {
        print $token->as_is;
    }
}
[download]

(update: forgot to include the assignment to $_)