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

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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://bugzilla.bioperl.org/ Email allenday@ucla.edu 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