NAME
Bio::Mitomaster::RNASeq - An mtDNA transcript.
SYNOPSIS
Generally, these objects are instantiated by calling the transcribe method on a Bio::Mitomaster::Seq object. If for some reason you want to create an RNASeq object directly, you must specify a SpeciesRef object, locus ID, and a hash reference of variants. If the sequence is partial, then you must also specify the start and end values. When created using the transcribe method, an RNASeq object will inherit the SpeciesRef object from the Seq object that creates it.
use Bio::Mitomaster::SpeciesRef;
use Bio::Mitomaster::RNASeq;
my $ref = Bio::Mitomaster::SpeciesRef->new(species=>'human', reference=>'rCRS');
my $rna_seq1 = Bio::Mitomaster::RNASeq->new(species_ref=>$ref, locus_id=>5, variants=>{1=>'T',2=>'T'});
my $rna_seq2 = Bio::Mitomaster::RNASeq->new(species_ref=>$ref, locus_id=>5, variants=>{1=>'T',2=>'T'}, start=>1, end=>15); #same thing except that we only have the first 15 nucleotides
my $s = $rna_seq1->seq(1,5); #$s is 'TTTCA', the first 5 RNA nucleotides of the transcript from locus 5;
ATTRIBUTES
See Bio::Mitomaster::MitoSeq for inherited attributes.
end
The end position of the sequence. Defaults to the length of the reference sequence transcript. Set this in order to analyze partial sequences. It will also cause the ref_seq value to end at this position.
locus_id
The locus_id for this RNA sequence. Use a Mitomaster object to see a list of the valid locus_id values that can be used (see the Bio::Mitomaster documentation).
start
The start position of the sequence. Defaults to 1. Set this in order to analyze partial sequences. It will also alter the behavior of the ref_seq method.
METHODS
See Bio::Mitomaster::MitoSeq for inherited methods, particularly the seq method, which is probably the most important one provided.
translate
Returns a Bio::Mitomaster::AASeq object representing the translation that would be produced by translating the transcript sequence of this object. This method cannot be called on partial transcript sequences. Normally, you would begin with a Bio::Mitomaster object and use its seq method to produce a Seq object. Then use the transcribe method of the Seq object to produce and RNASeq object, and finally use the translation method of the RNASeq object to produce an AASeq object.
AUTHOR
Marty Brandon, <mbrandon at uci.edu>
BUGS
Please report any bugs or feature requests to bug-bio-mitomaster-seq at rt.cpan.org
, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Mitomaster-RNASeq. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc Bio::Mitomaster::RNASeq
You can also look for information at:
RT: CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Mitomaster-RNASeq
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
Search CPAN
ACKNOWLEDGEMENTS
COPYRIGHT & LICENSE
Copyright 2009 Marty Brandon, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.