Bio::Variation::AAChange(3pm) User Contributed Perl Documentation Bio::Variation::AAChange(3pm)
NAME
Bio::Variation::AAChange - Sequence change class for polypeptides
SYNOPSIS
$aamut = Bio::Variation::AAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-proof' => $proof,
'-isMutation' => 1,
'-mut_number' => $mut_number
);
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$aamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$aachange->add_Allele($a2);
$aachange->allele_mut($a2);
print "
";
# add it to a SeqDiff container object
$seqdiff->add_Variant($rnachange);
# and create links to and from RNA level variant objects
$aamut->RNAChange($rnachange);
$rnachange->AAChange($rnachange);
DESCRIPTION
The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in
superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details.
If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See
Bio::Variation::AAChange 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://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 _
RNAChange
Title : RNAChange
Usage : $mutobj = $self->RNAChange;
: $mutobj = $self->RNAChange($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
similarity_score
Title : similarity_score
Usage : $self->similarity_score
Function: Measure for evolutionary conservativeness
of single amino substitutions. Uses BLOSUM62.
Negative numbers are noncoservative changes.
Returns : integer, undef if not single amino acid change
trivname
Title : trivname
Usage : $self->trivname
Function:
Given a Bio::Variation::AAChange object with linked
Bio::Variation::RNAChange and Bio::Variation::DNAMutation
objects, this subroutine creates a string corresponding to
the 'trivial name' of the mutation. Trivial name is
specified in Antonorakis & MDI Nomenclature Working Group:
Human Mutation 11:1-3, 1998.
Returns : string
perl v5.14.2 2012-03-02 Bio::Variation::AAChange(3pm)