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(), "\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";

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://github.com/bioperl/bioperl-live/issues

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    :