Bio::SeqFeature::Gene::Exon - a feature representing an exon # obtain an exon instance $exon somehow print "exon from ", $exon->start(), " to ", $exon->end(), " on seq ", $exon->seq_id(), ", strand ", $exon->strand(), ", encodes the peptide sequence ", $exon->cds()->translate()->seq(), "\n"; This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is coding. Supply -is_coding => 0 to the constructor or call $exon->is_coding(0) otherwise. Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email hlapp@gmx.net Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

is_coding
Title : is_coding Usage : if($exon->is_coding()) { # do something } if($is_utr) { $exon->is_coding(0); } Function: Get/set whether or not the exon codes for amino acid. Returns : TRUE if the object represents a feature translated into protein, and FALSE otherwise. Args : A boolean value on set.

primary_tag
Title : primary_tag Usage : $tag = $feat->primary_tag() $feat->primary_tag('exon') Function: Get/set the primary tag for the exon feature. This method is overridden here in order to allow only for tag values following a certain convention. For consistency reasons, the tag value must either contain the string 'exon' or the string 'utr' (both case-insensitive). In the case of 'exon', a string describing the type of exon may be appended or prefixed. Presently, the following types are allowed: initial, internal, and terminal (all case-insensitive). If the supplied tag value matches 'utr' (case-insensitive), is_coding() will automatically be set to FALSE, and to TRUE otherwise. Returns : A string. Args : A string on set.

location
Title : location Usage : my $location = $exon->location() Function: Returns a location object suitable for identifying the location of the exon on the sequence or parent feature. This method is overridden here to restrict allowed location types to non-compound locations. Returns : Bio::LocationI object Args : none

cds
Title : cds() Usage : $cds = $exon->cds(); Function: Get the coding sequence of the exon as a sequence object. The sequence of the returned object is prefixed by Ns (lower case) if the frame of the exon is defined and different from zero. The result is that the first base starts a codon (frame 0). This implementation returns undef if the particular exon is not translated to protein, i.e., is_coding() returns FALSE. Undef will also be returned if no sequence is attached to this exon feature. Returns : A Bio::PrimarySeqI implementing object. Args :