Bio::Variation::Allele(3) 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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AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org


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');
            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();
            Sets and returns the number of repeat units in the allele.
 Example : 
 Returns : string
 Args    : string


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


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