Toolbar

Summary

Bio::Tools::Gel - Calculates relative electrophoretic migration distances

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    use Bio::PrimarySeq;
    use Bio::Restriction::Analysis;
    use Bio::Tools::Gel;

    # get a sequence
    my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
    my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);

    # cut it with an enzyme
    my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
    @cuts = $ra->fragments('EcoRI'), 3;

    # analyse the fragments in a gel
    my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
    my %bands = $gel->bands;
    foreach my $band (sort {$b <=> $a} keys %bands){
      print $band,"\t", sprintf("%.1f", $bands{$band}),"\n";
    }

    #prints:
    #20   27.0
    #25   26.0
    #10   30.0

Description

This takes a set of sequences or Bio::Seq objects, and calculates their
respective migration distances using:
distance = dilation * (4 - log10(length(dna));
Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis.
CSHL Press, 1989.
Bio::Tools::Gel currently calculates migration distances based solely on
the length of the nucleotide sequence. Secondary or tertiary structure,
curvature, and other biophysical attributes of a sequence are currently
not considered. Polypeptide migration is currently not supported.

Methods

Methods description

 Title   : new
 Usage   : my $gel = Bio::Tools::Gel->new(-seq => $sequence,-dilate => 3);
 Function: Initializes a new Gel
 Returns : Bio::Tools::Gel
 Args    : -seq      => Bio::Seq(s), scalar(s) or list of either/both 
                        (default: none)
           -dilate   => Expand band migration distances (default: 1)

 Title   : add_band
 Usage   : $gel->add_band($seq);
 Function: Calls _add_band with a (possibly created) Bio::Seq object.
 Returns : 
 Args    : Bio::Seq, scalar sequence, or list of either/both.

 Title   : _add_band
 Usage   : $gel->_add_band($seq);
 Function: Adds a new band to the gel.
 Returns : 
 Args    : Bio::Seq object

 Title   : dilate
 Usage   : $gel->dilate(1);
 Function: Sets/retrieves the dilation factor.
 Returns : dilation factor 
 Args    : Float or none

 Title   : bands
 Usage   : $gel->bands;
 Function: Calculates migration distances of sequences.
 Returns : hash of (seq_id => distance)
 Args    :

 Title   : log10
 Usage   : log10($n);
 Function: returns base 10 log of $n.
 Returns : float
 Args    : float

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($seqs,$dilate) = $self->_rearrange([qw(SEQ DILATE)],
					  @args);
  if( ! ref($seqs)  ) {
      $self->add_band([$seqs]);
  } elsif( ref($seqs) =~ /array/i ||
	   $seqs->isa('Bio::PrimarySeqI') ) {
      $self->add_band($seqs);
  } 
  $self->dilate($dilate || 1);
  
  return $self;

}

sub add_band {

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

  foreach my $arg (@$args){
      my $seq;
      if( ! ref($arg) ) {
	  if( $arg =~ /^\d+/ ) {
	      $seq= Bio::PrimarySeq->new(-seq=>"N"x$arg, -id => $arg);
	  } else {
	      $seq= Bio::PrimarySeq->new(-seq=>$arg,-id=>length($arg));
	  }
      } elsif( $arg->isa('Bio::PrimarySeqI') ) {
	  $seq = $arg;
      } 

    $seq->validate_seq or $seq->throw("invalid symbol in sequence".$seq->seq()."\n");
    $self->_add_band($seq);
  }

}

sub _add_band {

  my($self,$arg) = @_;  
  if( defined $arg) {
      push (@{$self->{'bands'}},$arg);
  }

}

sub dilate {

  my($self,$arg) = @_;
  return $self->{dilate} unless $arg;
  $self->throw("-dilate should be numeric") if defined $arg and $arg =~ /[^e\d\.]/;
  $self->{dilate} = $arg;
  return $self->{dilate};

}

sub migrate {

  my ($self,$arg) = @_;
  $arg = $self unless $arg;
  if ( $arg ) {
      return 4 - log10($arg);
  } else { return 0; }

}

sub bands {

  my $self = shift;
  $self->throw("bands() is read-only") if @_;

  my %bands = ();
  
  foreach my $band (@{$self->{bands}}){
      my $distance = $self->dilate * migrate($band->length);
      $bands{$band->id} = $distance;
  }

  return %bands;

}

sub log10 {

    my $n = shift;
    return log($n)/log(10);
}

1;

}

General documentation

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

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

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email allenday@ucla.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _