Hi Rolf, many thanks for trying to help out and apologies if I seem to not get it... I tried your code (which I think is pretty much what I have now), and the error still the same.

use WWW::Mechanize();

while(<>)
{
if($_=~/^>(.*)/)
  {
    my $id=$1; 
    my  $seq=<>; chomp $seq; 

     print "$id\n";
     my $url = 'http://www.csbio.sjtu.edu.cn/bioinf/MemBrain/';  #what
+ I see in the browser, as you said
     my $mech = WWW::Mechanize->new();
     $mech->get($url);

     $mech->submit_form
     (
         form_name => 'myform',
         fields      => 
            {
                #textarea name | value
                S1 => ">$id\n$seq",

                #Radio button one with value (parameter 1)
                R4    =>  'TOPpre',

                #Radio button one with value (parameter 2)
                R2    =>  'SignalYES',

                #Radio button one with value (parameter 3)
                R3    =>  'Human',

                #Fill in email (parameter 4)
                email => 'myemail@gmail.com'
            }
        );
    }
}
[download]

The code executes until I print the id and then exits, with the error that I have posted earlier. I specified the form_name too, but nothing...