bionic (3) Bio::Tools::Gel.3pm.gz

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