/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqFeature::Gene::Intron

NAME

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

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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 - 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 : FAST::Bio::EnsEMBL::Exon
Args    :

downstream_Exon

Title   : downstream_Exon 
Usage   : $intron->downstream_Exon()
Function: exon downstream of the intron 
Returns : FAST::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 : FAST::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 : FAST::Bio::Seq
Args    : start and end