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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Tools::Gel \- Calculates relative electrophoretic migration distances .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 3 \& use Bio::PrimarySeq; \& use Bio::Restriction::Analysis; \& use Bio::Tools::Gel; \& \& # get a sequence \& my $d = \*(AqAAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG\*(Aq; \& my $seq1 = Bio::Seq\->new(\-id=>\*(Aqgroundhog day\*(Aq,\-seq=>$d); \& \& # cut it with an enzyme \& my $ra=Bio::Restriction::Analysis\->new(\-seq=>$seq1); \& @cuts = $ra\->fragments(\*(AqEcoRI\*(Aq), 3; \& \& # analyse the fragments in a gel \& my $gel = Bio::Tools::Gel\->new(\-seq=>\e@cuts,\-dilate=>10); \& my %bands = $gel\->bands; \& foreach my $band (sort {$b <=> $a} keys %bands){ \& print $band,"\et", sprintf("%.1f", $bands{$band}),"\en"; \& } \& \& #prints: \& #20 27.0 \& #25 26.0 \& #10 30.0 .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This takes a set of sequences or Bio::Seq objects, and calculates their respective migration distances using: distance = dilation * (4 \- log10(length(dna)); .PP Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis. \&\s-1CSHL\s0 Press, 1989. .PP 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. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Allen Day" .IX Header "AUTHOR - Allen Day" Email allenday@ucla.edu .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 7 \& 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) .Ve .SS "add_band" .IX Subsection "add_band" .Vb 5 \& 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. .Ve .SS "_add_band" .IX Subsection "_add_band" .Vb 5 \& Title : _add_band \& Usage : $gel\->_add_band($seq); \& Function: Adds a new band to the gel. \& Returns : \& Args : Bio::Seq object .Ve .SS "dilate" .IX Subsection "dilate" .Vb 5 \& Title : dilate \& Usage : $gel\->dilate(1); \& Function: Sets/retrieves the dilation factor. \& Returns : dilation factor \& Args : Float or none .Ve .SS "bands" .IX Subsection "bands" .Vb 5 \& Title : bands \& Usage : $gel\->bands; \& Function: Calculates migration distances of sequences. \& Returns : hash of (seq_id => distance) \& Args : .Ve .SS "log10" .IX Subsection "log10" .Vb 5 \& Title : log10 \& Usage : log10($n); \& Function: returns base 10 log of $n. \& Returns : float \& Args : float .Ve