Bio::SeqFeature::Gene::Intron(3pm)			User Contributed Perl Documentation			Bio::SeqFeature::Gene::Intron(3pm)

NAME

       Bio::SeqFeature::Gene::Intron - An intron feature

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here

FEEDBACK

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       Please direct usage questions or support issues to the mailing list:

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       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.

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AUTHOR - David Block
       Email dblock@gene.pbi.nrc.ca

APPENDIX

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

   upstream_Exon
	 Title	 : upstream_Exon
	 Usage	 : $intron->upstream_Exon()
	 Function: exon upstream of the intron
	 Returns : Bio::EnsEMBL::Exon
	 Args	 :

   downstream_Exon
	 Title	 : downstream_Exon
	 Usage	 : $intron->downstream_Exon()
	 Function: exon downstream of the intron
	 Returns : Bio::EnsEMBL::Exon
	 Args	 :

   phase
	 Title	 : phase
	 Usage	 : $intron->phase()
	 Function: returns the phase of the intron(where it interrupts the codon)
	 Returns : int(0,1,2)
	 Args	 :

   acceptor_splice_site
	 Title	 : acceptor_splice_site
	 Usage	 : $intron->acceptor_splice_site(21,3)
	 Function: returns the sequence corresponding to the
		   consensus acceptor splice site. If start and
		   end are provided, it will number of base pairs
		   left and right of the canonical AG. Here 21 means
		   21 bp into intron and 3 means 3 bp into the exon.
		   --Intron--21----|AG|-3-----Exon
		   Defaults to 21,3

	 Returns : Bio::Seq
	 Args	 : start and end

   donor_splice_site
	 Title	 : donor_splice_site
	 Usage	 : $intron->donor_splice_site(3,6)
	 Function: returns the sequence corresponding to the
		   consensus donor splice site. If start and
		   end are provided, it will number of base pairs
		   left and right of the canonical GT. Here 3 means
		   3 bp into exon and 6 means 6 bp into the intron.
		   --Exon-3--|GT|-6----Intron-
		   Defaults to 3,6

	 Returns : Bio::Seq
	 Args	 : start and end

perl v5.14.2							    2012-03-02					Bio::SeqFeature::Gene::Intron(3pm)