Mailing Lists¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

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¶

  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