...like I've already said: get rid of the \W+ in the substitution string:

$str =~ s/$query\W+/<em>$query<\/em> \W+/ig;
                                     ^^^
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The regex (i.e. s/$query\W+/) matches "perl: " which is then being substituted with the string "<em>$query</em> ".

Update: on second read it seems you want to keep the ":" (-> "ignore")...  in which case just don't match it in the first place, as ikegami said below.

What you may have had in mind could be written as

$str =~ s/$query(\W+)/<em>$query<\/em>$1/ig;
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that is, $1 would re-insert into the substitution string whatever the captured part in the regex (\W+) matched (i.e. ": ").  But as already said, that's not necessary if you don't include it in the match in the first place.