use Bio::EnsEMBL::Registry;

  my $reg = "Bio::EnsEMBL::Registry";
  $reg->load_registry_from_db(
      -host => "ensembldb.ensembl.org",
      -user => "anonymous");

  my $synteny_region_adaptor = $reg->get_adaptor(
      "Multi", "compara", "SyntenyRegion");

  $synteny_region_adaptor->store($synteny_region);

  my $synteny_region = $synteny_region_adaptor->fetch_by_dbID(1);
  my $synteny_regions = $synteny_region_adaptor->
      fetch_by_MethodLinkSpeciesSet_DnaFrag(
          $mlss, $dnafrag, $start, $end);

  use strict;
  use Bio::EnsEMBL::Registry;

  my $reg = "Bio::EnsEMBL::Registry";

  $reg->load_registry_from_db(
      -host=>"ensembldb.ensembl.org", -user=>"anonymous", -software_version => 38);

  my $method_link_species_set_adaptor = $reg->get_adaptor(
      "Multi", "compara", "MethodLinkSpeciesSet");
  my $human_mouse_synteny_method_link_species_set =
      $method_link_species_set_adaptor->
          fetch_by_method_link_type_registry_aliases(
              "SYNTENY", ["human", "mouse"]);

  my $genome_db_adaptor = $reg->get_adaptor(
      "Multi", "compara", "GenomeDB");
  my $genome_db = $genome_db_adaptor->
      fetch_by_name_assembly("Homo sapiens", undef);

  my $dnafrag_adaptor = $reg->get_adaptor(
      "Multi", "compara", "DnaFrag");
  my $dnafrag = $dnafrag_adaptor->
      fetch_by_GenomeDB_and_name($genome_db, "3");

  my $synteny_region_adaptor = $reg->get_adaptor(
      "Multi", "compara", "SyntenyRegion");
  my $synteny_regions = $synteny_region_adaptor->
      fetch_by_MethodLinkSpeciesSet_DnaFrag(
          $human_mouse_synteny_method_link_species_set,
          $dnafrag, 100000, 200000);

  foreach my $this_synteny_region (@$synteny_regions) {
    my $these_dnafrag_regions = $this_synteny_region->children();
    foreach my $this_dnafrag_region (@$these_dnafrag_regions) {
      print $this_dnafrag_region->dnafrag->genome_db->name, ": ", $this_dnafrag_region->slice->name, "\n";
    }
    print "\n";
  }

  my ($self, $mlss) = @_;

  if (!UNIVERSAL::isa($mlss, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet")) {
    throw("[$mlss] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
  }

  my $sql = "select sr.synteny_region_id from synteny_region sr where sr.method_link_species_set_id = ?";

  my $sth = $self->prepare($sql);
  $sth->execute($mlss->dbID);

  my $synteny_region_id;
  $sth->bind_columns(\$synteny_region_id);
  my @srs;
  while ($sth->fetch) {
    my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
    $sr->dbID($synteny_region_id);
    $sr->method_link_species_set_id($mlss->dbID);

    my $dfra = $self->db->get_DnaFragRegionAdaptor;
    my $dfrs = $dfra->fetch_by_synteny_region_id($synteny_region_id);
    while (my $dfr = shift @{$dfrs}) {
      $sr->add_child($dfr);
    }

    push @srs, $sr;
  }

  return\@ srs;
}

1;

  my ($self, $mlss, $dnafrag, $start, $end) = @_;

  if (!UNIVERSAL::isa($mlss, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet")) {
    throw("[$mlss] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
  }
  if (!UNIVERSAL::isa($dnafrag, "Bio::EnsEMBL::Compara::DnaFrag")) {
    throw("[$dnafrag] is not a Bio::EnsEMBL::Compara::DnaFrag object");
  }

  my $sql = "select sr.synteny_region_id from synteny_region sr, dnafrag_region dfr where sr.method_link_species_set_id = ? and sr.synteny_region_id=dfr.synteny_region_id and dfr.dnafrag_id = ?";
  
  if (defined $start) {
    $sql .= " and dfr.dnafrag_end >= $start";
  }
  if (defined $end) {
    $sql .= " and dfr.dnafrag_start <= $end";
  }

  my $sth = $self->prepare($sql);
  $sth->execute($mlss->dbID, $dnafrag->dbID);

  my $synteny_region_id;
  $sth->bind_columns(\$synteny_region_id);
  my @srs;
  while ($sth->fetch) {
    my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
    $sr->dbID($synteny_region_id);
    $sr->method_link_species_set_id($mlss->dbID);

    my $dfra = $self->db->get_DnaFragRegionAdaptor;
    my $dfrs = $dfra->fetch_by_synteny_region_id($synteny_region_id);
    while (my $dfr = shift @{$dfrs}) {
      $sr->add_child($dfr);
    }

    push @srs, $sr;
  }

  return\@ srs;

  my ($self, $method_link_species_set, $reference_slice) = @_;
  my $all_synteny_regions = []; # Returned value

  ## method_link_species_set will be checked in the fetch_all_by_MethodLinkSpeciesSet_DnaFrag method

  ## Check original_slice
  unless(UNIVERSAL::isa($reference_slice, 'Bio::EnsEMBL::Slice')) {
    throw("[$reference_slice] should be a Bio::EnsEMBL::Slice object\n");
  }

  my $dnafrag_adaptor = $self->db->get_DnaFragAdaptor;

  my $projection_segments = $reference_slice->project('toplevel');
  return [] if(!@$projection_segments);

  foreach my $this_projection_segment (@$projection_segments) {
    my $this_slice = $this_projection_segment->to_Slice;
    my $this_dnafrag = $dnafrag_adaptor->fetch_by_Slice($this_slice);
    next if (!$this_dnafrag);
    my $these_synteny_regions = $self->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
            $method_link_species_set,
            $this_dnafrag,
            $this_slice->start,
            $this_slice->end,
        );

    push (@$all_synteny_regions, @$these_synteny_regions);
  }

  return $all_synteny_regions;

  my $self = shift(@_);

  return $self->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(@_);

   my ($self,$dbID) = @_;

   if( !defined $dbID ) {
     throw("fetch_by_dbID with no dbID!");
   }

   my $sth = $self->prepare("select synteny_region_id, method_link_species_set_id from synteny_region where synteny_region_id = $dbID");
   $sth->execute;
   my ($synteny_region_id, $method_link_species_set_id) = $sth->fetchrow_array();

   my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
   $sr->dbID($synteny_region_id);
   $sr->method_link_species_set_id($method_link_species_set_id);

   my $dfra = $self->db->get_DnaFragRegionAdaptor;
   my $dfrs = $dfra->fetch_by_synteny_region_id($dbID);
   while (my $dfr = shift @{$dfrs}) {
     $sr->add_child($dfr);
   }
   return $sr;

   my ($self,$sr) = @_;

   if( !ref $sr || !$sr->isa("Bio::EnsEMBL::Compara::SyntenyRegion") ) {
       throw("$sr is not a SyntenyRegion object");
   }

   my $sth = $self->prepare("insert into synteny_region (method_link_species_set_id) VALUES (?)");
   
   $sth->execute($sr->method_link_species_set_id);
   my $synteny_region_id = $sth->{'mysql_insertid'};
   
   $sr->dbID($synteny_region_id);
   $sr->adaptor($self);
   
   my $dfra = $self->db->get_DnaFragRegionAdaptor;
   foreach my $dfr (@{$sr->children}) {
     $dfr->synteny_region_id($synteny_region_id);
     $dfra->store($dfr);
   }
   return $sr->dbID;

 - Bio::EnsEMBL::Compara::SyntenyRegion
 - Bio::EnsEMBL::Compara::DnaFragRegion
 - Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
 - Bio::EnsEMBL::Compara::GenomeDB