Use a list instead of a string: 

my @command = ( 'c:\\blast\bin\blastall', '-p', 'blastn', '-d', "$hu_s
+eq $hd_seq", '-i', $contig, '-o', $alignment );
print "@command\n";
0 == system @command or die "system @command failed: $?";

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In reply to Re: quoting issue with system command by jwkrahn
in thread quoting issue with system command by lomSpace

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