read your file line by line to a hash where the sequence will be the hash keys. each line you read check if the key isn't already exist in the hash, if it is than continue with the next line. it should be something like this:

my ($line, %hash);
while ($line = <FILE>) {
  if ($line =~ /(your_sequence_format)/) {
    if (! exists($hash{$1})) {
      $hash{$1} = $line;
    }
  }
}
# now you can print the hash back to your file
[download]

Thanks.

Hotshot