Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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

           # get a sequence
           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";

           #20   27.0
           #25   26.0
           #10   30.0


       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,

       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.


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AUTHOR - Allen Day



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

        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