Bio::SeqFeature::SiRNA::Oligo.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.

SYNOPSIS

   use Bio::SeqFeature::SiRNA::Oligo;
 
   my $oligo = Bio::SeqFeature::SiRNA::Oligo->
       new( -seq         => 'AUGCCGAUUGCAAGUCAGATT',
            -start       => 10,
            -end         => 31,
            -strand      => -1,
            -primary     => 'SiRNA::Oligo',
            -source_tag  => 'Bio::Tools::SiRNA',
            -tag         => { note => 'A note' }, );
 
   # normally two complementary Oligos are combined in an SiRNA::Pair
   # object
   $pair->antisense($oligo);
 
 

DESCRIPTION

Object methods for single SiRNA oligos - inherits Bio::SeqFeature::Generic. Does not include methods for designing SiRNAs - see Bio::Tools::SiRNA for that.

SEE ALSO

Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.

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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Donald Jackson (donald.jackson@bms.com)

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

   Title         : new
   Usage         : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new();
   Function      : Create a new SiRNA::Oligo object
   Returns       : Bio::Tools::SiRNA object
   Args          : -seq            sequence of the RNAi oligo.  Should be in RNA alphabet
                                   except for the final TT overhang.
                   -start          start position
                   -end            end position
                   -strand         strand
                   -primary        primary tag - defaults to 'SiRNA::Oligo'
                   -source         source tag
                   -score          score value
                   -tag            a reference to a tag/value hash
                   -seq_id         the display name of the sequence
                   -annotation     the AnnotationCollectionI object
                   -location       the LocationI object
 
 

Currently passing arguments in gff_string or gff1_string is not supported. SiRNA::Oligo objects are typically created by a design algorithm such as Bio::Tools::SiRNA

seq

   Title         : Seq
   Usage         : my $oligo_sequence = $sirna_oligo->seq();
   Purpose       : Get/set the sequence of the RNAi oligo
   Returns       : Sequence for the RNAi oligo
   Args          : Sequence of the RNAi oligo (optional)
   Note          : Overloads Bio::SeqFeature::Generic seq method - the oligo and 
                   parent sequences are different. 
                   Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
                   SiRNA::Pair objects are typically created by a design algorithm such as
                   Bio::Tools::SiRNA.