Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::SeqFeature::Gene::Intron.3pm

NAME

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:

   http://bugzilla.open-bio.org/
 
 

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