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lib/Bio/Tools/Run/FootPrinter.pm  view on Meta::CPAN

=head1 SYNOPSIS

  use Bio::Tools::Run::FootPrinter;

  my @params = (size => 10,
                 max_mutations_per_branch => 4,
                 sequence_type => 'upstream',
                 subregion_size => 30,
                 position_change_cost => 5,
                 triplet_filtering => 1,
                 pair_filtering => 1,
                 post_filtering => 1,
                 inversion_cost => 1,
                 max_mutations => 4,
                 tree => "~/software/FootPrinter2.0/tree_of_life" );

  my $fp = Bio::Tools::Run::FootPrinter->new(@params, -verbose => 1);

  my $sio = Bio::SeqIO->new(-file => "seq.fa", -format => "fasta");

  while (my $seq = $sio->next_seq){
    push @seq, $seq;
  }
  my @fp = $fp->run(@seq);

  foreach my $result(@fp){
    print "***************\n".$result->seq_id."\n";
    foreach my $feat($result->sub_SeqFeature){
      print $feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
    }
  }

=head1 DESCRIPTION

From the FootPrinter manual:

FootPrinter is a program that performs phylogenetic footprinting. 
It takes as input a set of unaligned orthologous sequences from various 
species, together with a phylogenetic tree relating these species. 
It then searches for short regions of the sequences that are highly conserved, 
according to a parsimony criterion. 

The regions identified are good candidates for regulatory elements. 
By default, the program searches for regions that are well conserved across 
all of the input sequences, but this can be relaxed to 
find regions conserved in only a subset of the species

=head2 About Footprinter

Written by Mathieu Blanchette and Martin Tompa. Available here:

  http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz 


=head2 Running Footprinter

To run FootPrinter, you will need to set the environment variable
FOOTPRINTER_DIR to where the binary is located (even if the executable
is in your path). For example:

  setenv FOOTPRINTER_DIR /usr/local/bin/FootPrinter2.0/


=head2 Available Parameters

  PARAM         VALUES        DESCRIPTION
  ------------------------------------------------------------------------
  tree                      <file>     REQUIRED, Tree in Newick Format
                                       to evaluate parsimony score 
                                       REQUIRED unless tree_of_life
                                       exists in FOOTPRINTER_DIR
  sequence_type             upstream   Default upstream
                            downstream
                            other
  size                      4-16       Specifies the size of the motifs sought
  max_mutations             0-20       maximum parsimony score allowed for the motifs
  max_mutations_per_branch  0-20       Allows at most a fixed number of mutations per 
                                       branch of the tree
  losses                    <file>     files give span constraints so that the motifs
                                       reported are statistically significant
                                       Example files
                                       universal([6-9]|1[0-2])(loose|tight)?.config
                                       come with FootPrinter2.0.
                                       Install these in FOOTPRINTER_DIR and use by
                                       setting "losses" to "somewhat significant",
                                       "significant", or "very significant". Do not
                                       set loss_cost.
  loss_cost                 0-20       a cost associated with losing a motif along some 
                                       branch of the tre
  subregion_size            1-infinity penalize motifs whose position in the sequences 
                                       varies too much
  position_change_cost      0-20       Cost for changing subregion
  triplet_filtering         1/0        pre-filtering step that removes from consideration 
                                       any substring that does not have a sufficiently good 
                                       pair of matching substrings in some pair of the other 
                                       input sequences
  pair_filtering            1/0        Same as triplet filtering, but looks only for one match 
                                       per other sequence
  post_filtering            1/0        when used in conjunction with the triplet filtering 
                                       option, this often significantly speeds up the program, 
                                       while still garanteeing optimal results
  indel_cost                1-5        insertions and deletions will be allowed in the motifs 
                                       sought, at the given cost
  inversion_cost            1-5        This option allows for motifs to undergo inversions, 
                                       at the given cost. An inversion reverse-complements 
                                       the motif.
  details                   1/0        Shows some of the details about the progress of the 
                                       computation
  html                      1/0        produce html output (never deleted)
  ps                        1/0        produce postscript output (never deleted)

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists