Bio::Tools::Gel.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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