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my %targets = map {/(.*)/; ($1, 1)} <INPUTDOMAINLIST>;
my @neighbours = @domain1[grep {$_ > 0 && $targets{$domain[$_-1]} || $
+_ < $#domain1 && $targets{$domain[$_+1]}} 0..$#domain];

my %neighbours;
for (my $i = 0; $i < @domain1; $i++) {
...
    push @{$neighbours{$domain[$i]}}, $neighbours{$domain[$i+1]} if $i
+ < $#domain1;
}
my @neighbours = map {@$_} @neighbours{map {/(.*)/; $1} <INPUTDOMAINLI
+ST>};