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
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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)