Alternative method - Read the file in as one slurp, and count the number of occurrences of each term.

Something like this:

# read terms file
open (SRC, $searchTermsFile) || die "can't open search terms file";
@terms = <SRC>;
chomp (@terms);
# read annotations file...
open(my $f, '<', $file) or die "OPENING $file: $!\n";
my $string = do { local($/); <$f> };
close($f);

my %nTermHits;

foreach my $term (@terms) {
   $nTermHits{$term} = () = $string =~ /\b$term\b/ig;
}
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I don't have PERL on this machine so any minor syntax issues are your problem :o)