#!/usr/bin/perl -w
# get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  $f = Bio::Factory::EMBOSS -> new();
  # get an EMBOSS application  object from the factory
  $water = $f->program('water');

  # here is an example of running the application -
  # water can compare 1 sequence against 1 or more sequences
  # in a database using Smith-Waterman
  my $seq_to_test = 'atgcatgcatgc'; # this would have a seq here
  my @seqs_to_check = ('atgcatgc'); # this would be a list of seqs to compare 
                       # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({-sequences => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
}