|Bio::Variation::Allele(3pm)||User Contributed Perl Documentation||Bio::Variation::Allele(3pm)|
Bio::Variation::Allele - Sequence object with allele-specific attributes
$allele1 = Bio::Variation::Allele->new ( -seq => 'A', -id => 'AC00001.1', -alphabet => 'dna', -is_reference => 1 );
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details.
Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too.
A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string.
In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7).
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 lists Your participation is much appreciated.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
AUTHOR - Heikki Lehvaslaiho¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : is_reference Usage : $obj->is_reference() Function: sets and returns boolean values. Unset values return false. Example : $obj->is_reference() Returns : boolean Args : optional true of false value
Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args :
Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args :
Title : repeat_unit Usage : $obj->repeat_unit('ca'); Function: Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string
Title : repeat_count Usage : $obj->repeat_count(); Function: Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string
Title : count Usage : $obj->count(); Function: Sets and returns the number of times this allele was observed. Example : Returns : string Args : string
Title : frequency Usage : $obj->frequency(); Function: Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string