Bio::SeqFeature::Gene::Intron - An intron feature
Give standard usage here
Describe the object here
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : upstream_Exon Usage : $intron->upstream_Exon() Function: exon upstream of the intron Returns : Bio::EnsEMBL::Exon Args :
Title : downstream_Exon Usage : $intron->downstream_Exon() Function: exon downstream of the intron Returns : Bio::EnsEMBL::Exon Args :
Title : phase Usage : $intron->phase() Function: returns the phase of the intron(where it interrupts the codon) Returns : int(0,1,2) Args :
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
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