NAME

Bio::Variation::DNAMutation - DNA level mutation class

SYNOPSIS

    $dnamut = Bio::Variation::DNAMutation->new
        ('-start'         => $start,
         '-end'           => $end,
         '-length'        => $len,
         '-upStreamSeq'   => $upflank,
         '-dnStreamSeq'   => $dnflank,
         '-proof'         => $proof,
         '-isMutation'    => 1,
         '-mut_number'    => $mut_number
        );
    $a1 = Bio::Variation::Allele->new;
    $a1->seq('a');
    $dnamut->allele_ori($a1);
    my $a2 = Bio::Variation::Allele->new;
    $a2->seq('t');
    $dnamut->add_Allele($a2);

    print "Restriction changes are ", $dnamut->restriction_changes, "\n";

    # add it to a SeqDiff container object
    $seqdiff->add_Variant($dnamut);

DESCRIPTION

The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details.

If the variation described by a DNAMutation object is transcibed, link the corresponding Bio::Variation::RNAChange object to it using method RNAChange(). See Bio::Variation::RNAChange for more information.

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://github.com/bioperl/bioperl-live/issues

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 _

CpG

 Title   : CpG
 Usage   : $obj->CpG()
 Function: sets and returns boolean values for variation
           hitting a CpG site.  Unset value return -1.
 Example : $obj->CpG()
 Returns : boolean
 Args    : optional true of false value

RNAChange

 Title   : RNAChange
 Usage   : $mutobj = $obj->RNAChange;
         : $mutobj = $obj->RNAChange($objref);
 Function: Returns or sets the link-reference to a mutation/change object.
           If there is no link, it will return undef
 Returns : an obj_ref or undef

label

 Title   : label
 Usage   : $obj->label();
 Function:

            Sets and returns mutation event label(s).  If value is not
            set, or no argument is given returns false.  Each
            instantiable subclass of L<Bio::Variation::VariantI> needs
            to implement this method. Valid values are listed in
            'Mutation event controlled vocabulary' in
            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

 Example :
 Returns : string
 Args    : string

sysname

 Title   : sysname
 Usage   : $self->sysname
 Function:

           This subroutine creates a string corresponding to the
           'systematic name' of the mutation. Systematic name is
           specified in Antonorakis & MDI Nomenclature Working Group:
           Human Mutation 11:1-3, 1998.

 Returns : string