The Seed Servers are a newer way of accessing the SEED, but at the moment they are limited to the Argonne SEED. Rather than the SOAP based approach which is designed around a single call, the SEED servers are designed around sending larger chunks of data. If you are interested in using the SEED servers I have included a short demo in the read more.

Typically you send a hash of IDs to a function, and it returns a hash with the original IDs and the result of your call. On octopussy the perl modules to access the SEED servers are in /usr/local/genome/seed-servers/ and the appropriate path’s are set for you. All you need to do is import the modules and you are off. This is some example code that should demonstrate how to retrieve all functions for all proteins in all complete prokaryotic genomes.

use strict;
use SAPserver;
my $sap=new SAPserver;
my $all_genomes = $sap->all_genomes(-prokaryotic=>1, -complete=>1);
my $all_pegs = $sap->all_features({
                -ids => [ keys %$all_genomes ],
                -type => [ 'peg' ],
                });
foreach my $genome (keys %$all_pegs) {
        my $functions = $sap->ids_to_functions({
                -ids => $all_pegs->{$genome},
                });
        foreach my $peg (keys %$functions) {
                print "$pegt", $functions->{$peg}, "n";
        }
}

This is the full documentation for the SAP server, and it will just take some practise to figure out what methods do and what they return. If you are unsure, use Data::Dumper!