Bio::Tools::Spidey::Exon(3pm)				User Contributed Perl Documentation			     Bio::Tools::Spidey::Exon(3pm)

NAME

       Bio::Tools::Spidey::Exon - A single exon determined by an alignment

SYNOPSIS

	 # See Bio::Tools::Spidey::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(), "
";

	 # the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
	 print "exon from ", $exon->feature1()->start(),
	       " to ", $exon->feature1()->end(), "
";
	 # also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
	 print "exon from ", $exon->query()->start(),
	       " to ", $exon->query()->end(), "
";

	 # coordinates on the matching EST (recommended way):
	 print "matches on EST from ", $exon->est_hit()->start(),
	       " to ", $exon->est_hit()->end(), "
";

	 # the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
	 print "matches on EST from ", $exon->feature2()->start(),
	       " to ", $exon->feature2()->end(), "
";
	 # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
	 print "exon from ", $exon->subject()->start(),
	       " to ", $exon->subject()->end(), "
";

DESCRIPTION

       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 Spidey 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 est_hit().

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
	to one of the Bioperl mailing lists.  Your participation is much appreciated.

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

   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 the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ryan Golhar
       Email golharam@umdnj.edu

APPENDIX

       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
	Function: This is the percent id as reported by Spidey
	Returns : value of percentage_id
	Args	:

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

   mismatches
	Title	: mismatches
	Usage	: $obj->mismatches;
	Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this
		  exon (i.e., genomic region).
	Returns : value of mismatches.
	Args	:

   gaps
	Title	: gaps
	Usage	: $obj->gaps;
	Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this
		  exon (i.e., genomic region).
	Returns : value of gaps.
	Args	:

   donor
	Title	: donor
	Usage	: $obj->donor;
	Function: Returns 0 if a splice donor site does not exist, or
		  1 if a splice donor site exists
	Returns : value of existence of donor splice site (0 or 1)
	Args	:

   acceptor
	Title	: acceptor
	Usage	: $obj->acceptor;
	Function: Returns 0 if a splice acceptor site does not exist, or
		  1 if a splice acceptor site exists
	Returns : value of existence of acceptor splice site (0 or 1)
	Args	:

perl v5.14.2							    2012-03-02					     Bio::Tools::Spidey::Exon(3pm)