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.\" ========================================================================
.\"
.IX Title "Bio::SeqFeature::SiRNA::Oligo 3pm"
.TH Bio::SeqFeature::SiRNA::Oligo 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SeqFeature::SiRNA::Oligo \- Perl object for small inhibitory RNAs.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::SeqFeature::SiRNA::Oligo;
\&
\&  my $oligo = Bio::SeqFeature::SiRNA::Oligo\->
\&      new( \-seq         => \*(AqAUGCCGAUUGCAAGUCAGATT\*(Aq,
\&           \-start       => 10,
\&           \-end         => 31,
\&           \-strand      => \-1,
\&           \-primary     => \*(AqSiRNA::Oligo\*(Aq,
\&           \-source_tag  => \*(AqBio::Tools::SiRNA\*(Aq,
\&           \-tag         => { note => \*(AqA note\*(Aq }, );
\&
\&  # normally two complementary Oligos are combined in an SiRNA::Pair
\&  # object
\&  $pair\->antisense($oligo);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Object methods for single SiRNA oligos \- inherits
Bio::SeqFeature::Generic.  Does \fBnot\fR include methods for designing
SiRNAs \- see Bio::Tools::SiRNA for that.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Donald Jackson (donald.jackson@bms.com)
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\&  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 \*(AqSiRNA::Oligo\*(Aq
\&                  \-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
.Ve
.PP
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
.SS "seq"
.IX Subsection "seq"
.Vb 10
\&  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.
.Ve