why not use a hash instead of an array? untested: 
%hash = map { $_ => 1 } @array;
open (FILE, $file) or die "blah";
while (<FILE>) {
  my $key = (split("\t",$_))[2];
  next unless ($hash{$key});
  # do processing of line here ...
}

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In reply to Re: Efficiently compare sorted array vs another sorted array and pattern match by eXile
in thread Efficiently compare sorted array vs another sorted array and pattern match by mdog

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