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

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,"\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.

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		    Bio::Tools::Gel(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Allen Day | APPENDIX

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