/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::Gel

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