Bio::Tools::Sim4::Exon - A single exon determined by an alignment # See Bio::Tools::Sim4::Results for a description of the context. # an instance of this class is-a Bio::SeqFeature::SimilarityPair # coordinates of the exon (recommended way): print "exon from ", $exon->start(), " to ", $exon->end(), "\n"; # the same (feature1() inherited from Bio::SeqFeature::FeaturePair) print "exon from ", $exon->feature1()->start(), " to ", $exon->feature1()->end(), "\n"; # also the same (query() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->query()->start(), " to ", $exon->query()->end(), "\n"; # coordinates on the matching EST (recommended way): print "matches on EST from ", $exon->est_hit()->start(), " to ", $exon->est_hit()->end(), "\n"; # the same (feature2() inherited from Bio::SeqFeature::FeaturePair) print "matches on EST from ", $exon->feature2()->start(), " to ", $exon->feature2()->end(), "\n"; # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->subject()->start(), " to ", $exon->subject()->end(), "\n"; This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by aligning an EST sequence (using Sim4 in this case). Consequently, the notion of query and subject is always from the perspective of the genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon->start(), $exon->end() etc will always return what you expect. To get the coordinates on the matching EST, refer to the properties of the feature returned by the est_hit manpage().

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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://bio.perl.org/bioperl-bugs/ Email birney@sanger.ac.uk Hilmar Lapp <hlapp@gmx.net> or <hilmar.lapp@pharma.novartis.com>. Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

percentage_id
Title : percentage_id Usage : $obj->percentage_id($newval) Function: This is a synonym for 100 * $obj->est_hit()->frac_identical(). Returns : value of percentage_id Args : newvalue (optional)

est_hit
Title : est_hit Usage : $est_feature = $obj->est_hit(); Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this exon (i.e., genomic region). At present, merely a synonym for $obj->feature2(). Returns : An Bio::SeqFeatureI implementing object. Args :