Ewan Birney

NAME

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

SYNOPSIS

    #An example of a virtual restriction digest and subsequent gel run
    use Bio::Seq;
    use Bio::Tools::RestrictionEnzyme;
    use Bio::Tools::Gel;

    my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
    my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);
    my $EcoRI = Bio::Tools::RestrictionEnzyme->new(-NAME=>'EcoRI');
    my @cuts = $EcoRI->cut_seq($seq);

    my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
    my %bands = $gel->bands;
    foreach my $band (keys %bands){
      print $band,"\t",$bands{$band},"\n";
    }

    #prints:
    #25      26.0205999132796
    #10      30
    #20      26.9897000433602

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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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 = new Bio::Tools::Gel(-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