/ 
bioperl-1.2.3
/ Bio::Variation::Allele

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://bio.perl.org/MailList.html             - About the mailing lists

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/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom

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
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    :

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