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).

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Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

is_reference
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

add_DBLink
Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args :

each_DBLink
Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args :

repeat_unit
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

repeat_count
Title : repeat_count Usage : $obj->repeat_count(); Function: Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string

count
Title : count Usage : $obj->count(); Function: Sets and returns the number of times this allele was observed. Example : Returns : string Args : string

frequency
Title : frequency Usage : $obj->frequency(); Function: Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string