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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://github.com/bioperl/bioperl-live/issues

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