Christopher Fields > BioPerl-1.6.901 > Bio::Tools::Gel

Download:
BioPerl-1.6.901.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.923

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://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
syntax highlighting: