The following would be more appropriate:

my $seq;
...

if (defined($ENV{GATEWAY_INTERFACE})) {
   # We were called via CGI.
   my $cgi = new CGI;
   $seq = $cgi->param('Sequence_input');
   ...
}
else
{  
   GetOptions(
      "sequence=s" => \$seq,
      ...
   );
}
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