use strict;
use autodie;

open my $FH, '<', 'test.dat';
open my $FH2, '>', 'seq.dat';

for (do {local $/ = ""; <$FH>}) {
	my ($name) = /Name:\s+(.+)/;
	my ($seq) = /Nucleotide\sSequence:\s(.*)/xms;
	$seq =~ s/\n//g;
	print $FH2 "$name\n$seq\n\n";
}