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bio::seqfeature::sirna::oligo(3pm) [debian man page]

Bio::SeqFeature::SiRNA::Oligo(3pm)			User Contributed Perl Documentation			Bio::SeqFeature::SiRNA::Oligo(3pm)

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:

	 https://redmine.open-bio.org/projects/bioperl/

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.

perl v5.14.2							    2012-03-02					Bio::SeqFeature::SiRNA::Oligo(3pm)

Check Out this Related Man Page

Bio::Tools::SiRNA::Ruleset::saigo(3pm)			User Contributed Perl Documentation		    Bio::Tools::SiRNA::Ruleset::saigo(3pm)

NAME

       Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs

SYNOPSIS

       Do not use this module directly.  Instead, use Bio::Tools::SiRNA and specify the saigo ruleset:

	 use Bio::Tools::SiRNA;

	 my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
						      -rules  => 'saigo'
	   );
	 my @pairs = $sirna_designer->design;

	 foreach $pair (@pairs) {
	     my $sense_oligo_sequence = $pair->sense->seq;
	     my $antisense_oligo_sequence = $pair->antisense->seq;

	     # print out results
	     print join ("	", $pair->start, $pair->end, $pair->rank,
			 $sense_oligo_sequence, $antisense_oligo_sequence), "
";
	 }

DESCRIPTION

       This package implements the rules for designing siRNA reagents published by Ui-Tei et al(2004).  The rules are:

       1.   The first base in the sense strand of the duplex must be a G or C

       2.   The first base in the antisense strand of the duplex must be an A or U

       3.   The first 7 nucleotides in the antisense strand of the duplex must be A or U

       4.   There cannot be more than 9 consecutive G or C nucleotides

       5.   The first 12 nucleotides in the sense strand of the duplex should have 33-66% GC

       The module inherits from Bio::Tools::SiRNA.  See the documentation for that module for information on how to specify the target and recover
       the SiRNA duplex information.

   EXPORT
       None.

SEE ALSO

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

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:

	 https://redmine.open-bio.org/projects/bioperl/

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	: Do not call directly - use Bio::Tools::SiRNA->new instead.
	 Returns : Bio::Tools::SiRNA::Ruleset::saigo object
	 Args  : none

perl v5.14.2							    2012-03-02				    Bio::Tools::SiRNA::Ruleset::saigo(3pm)
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