Bio::Variation::Allele(3pm)				User Contributed Perl Documentation			       Bio::Variation::Allele(3pm)

NAME

       Bio::Variation::Allele - Sequence object with allele-specific attributes

SYNOPSIS

	 $allele1 = Bio::Variation::Allele->new ( -seq => 'A',
						  -id  => 'AC00001.1',
						  -alphabet => 'dna',
						  -is_reference => 1
						);

DESCRIPTION

       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).

FEEDBACK

   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 lists  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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 the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

APPENDIX

       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

perl v5.14.2							    2012-03-02					       Bio::Variation::Allele(3pm)