$a = 'PF01389    6    218    1    255    430.09';
$b = 'PF00691    PF01389';

my @a = split ' ', $a;
my @b = split ' ', $b;

my %a; @a{@a} = ();

my @common = grep { exists $a{$_} } @b;

##</code><code>##

my $pattern = $b; # so as not to bash $b
$pattern =~ s/\s+/|/g;

@common = " $a " =~ /\s($pattern)\s/g;

##</code><code>##

my $pattern = join '|', map quotemeta($_), split ' ', $b;
@common = " $a " =~ /\s($pattern)\s/g;