Better: 
my @command = ("c:\\blast\bin\\blastall.exe",
   -p => 'blastn',
   -d => "$hu_seq $hd_seq",
   -i => $contig,
   -o => $alignment,
);
system(@command);

[download]

Note: You've got a problem if -d expects space-separated paths if the paths have spaces in them.

In reply to Re^5: quoting issue with system command by ikegami
in thread quoting issue with system command by lomSpace

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