BEGIN{
  ${^RE_TRIE_MAXBUF} = 0;
}

##</code><code>##

@proteinNames = ...;

my %res;

m[^(\S+)] and push @{ $res{ $1 } }, $_ for @proteinNames;

$res{ $_ } = join '|', reverse sort map { quotemeta } @{ $res{ $_ } }
    for keys %res;
    
while( my $line = <> ) {
    for my $key ( keys %res ) {
        if( $line =~ $key ) {
            $line =~ s[($re{ $key })][\*\*$1\*\*]ig;
            print $line;
        }
    }
}