| Bio::Tools::Gel(3pm) | User Contributed Perl Documentation | Bio::Tools::Gel(3pm) |
Bio::Tools::Gel - Calculates relative electrophoretic migration distances
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
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
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.
Title : _add_band Usage : $gel->_add_band($seq); Function: Adds a new band to the gel. Returns : Args : Bio::Seq object
Title : dilate Usage : $gel->dilate(1); Function: Sets/retrieves the dilation factor. Returns : dilation factor Args : Float or none
Title : bands Usage : $gel->bands; Function: Calculates migration distances of sequences. Returns : hash of (seq_id => distance) Args :
Title : log10 Usage : log10($n); Function: returns base 10 log of $n. Returns : float Args : float
| 2018-10-27 | perl v5.26.2 |