Bio::Tools::Gel(3pm)					User Contributed Perl Documentation				      Bio::Tools::Gel(3pm)

NAME

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

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,"	", sprintf("%.1f", $bands{$band}),"
";
	   }

	   #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.

FEEDBACK

   Mailing Lists
       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

   Support
       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.

   Reporting Bugs
       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/

AUTHOR - Allen Day
       Email allenday@ucla.edu

APPENDIX

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

   new
	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)

   add_band
	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.

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

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

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

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

perl v5.14.2							    2012-03-02						      Bio::Tools::Gel(3pm)