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Bio-Mitomaster-0.10
River stage zero No dependents
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/ Bio::Mitomaster::Seq

NAME

Bio::Mitomaster::Seq - An mtDNA sequence.

SYNOPSIS

These objects should almost always be instantiated by calling the seq method on a Bio::Mitomaster object. Each Seq object has an associated SpeciesRef object (inherited attribute from MitoSeq). The SpeciesRef is an internal reference for meta-data, such as locus positions and the reference sequence. A Seq is specific for a particular species and reference sequence, and once instantiated the context cannot be changed. To create a Seq object you must provide the SpeciesRef, a hash of variants, and the start and end values of the sequence. Bio::Mitomaster encapsulates the logic of creating the right SpeciesRef object, reading seqs from files, and performing the needed alignment.

    use Bio::Mitomaster::SpeciesRef;
    use Bio::Mitomaster::Seq;

    my $ref = Bio::Mitomaster::SpeciesRef->new(species=>'human', reference=>'rCRS');
    my $seq1 = Bio::Mitomaster::Seq->new(species_ref=>$ref, variants=>{1=>'T',2=>'T'});
    my $seq2 = Bio::Mitomaster::Seq->new(species_ref=>$ref, variants=>{1=>'T',2=>'T'}, start=>1, end=>577); #same thing except that we only have the first 577 nucleotides

    my $s = $seq1->seq(1,5);  #$s is 'TTTCA';
    my $r_seq = $seq1->transcribe(1);  #$r_seq is an RNASeq object containing the transcript for the locus with ID 1.

ATTRIBUTES

See Bio::Mitomaster::MitoSeq for inherited attributes.

METHODS

See Bio::Mitomaster::MitoSeq for inherited methods, particularly the seq method, which is probably the most important one provided.

transcribe($locus_id)

Returns a Bio::Mitomaster::RNASeq object representing the transcript that would be produced by transcribing the locus identified by $locus_id. The boundaries of the locus to transcribe are retrieved from the species_ref attribute (a Bio::Mitomaster::SpeciesRef object). If the locus boundaries fall outside the sequence start and end values an error is returned. The RNA sequence returned within the RNASeq object is adjusted for all expected natural processes (poly-adenylation, uracil replaces thymine, etc.).

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-Seq. 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::Seq

You can also look for information at:

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.