NAME

       Ace::Sequence::Transcript - Simple "Gene" Object

SYNOPSIS

           # open database connection and get an Ace::Object sequence
           use Ace::Sequence;

           # get a megabase from the middle of chromosome I
           $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                                     -db     => $db,
                                     -offset => 3_000_000,
                                     -length => 1_000_000);

           # get all the transcripts
           @genes = $seq->transcripts;

           # get the exons from the first one
           @exons = $genes[0]->exons;

           # get the introns
           @introns = $genes[0]->introns

           # get the CDSs (NOT IMPLEMENTED YET!)
           @cds = $genes[0]->cds;

DESCRIPTION

       Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature.  It inherits all the methods of
       Ace::Sequence::Feature, but adds the ability to retrieve the annotated introns and exons of the gene.

OBJECT CREATION

       You will not ordinarily create an Ace::Sequence::Gene object directly.  Instead, objects will be created
       in response to a transcripts() call to an Ace::Sequence object.

OBJECT METHODS

       Most methods are inherited from Ace::Sequence::Feature.  The following methods are also supported:

       exons()
             @exons = $gene->exons;

           Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.

       introns()
             @introns = $gene->introns;

           Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.

       cds()
             @cds = $gene->cds;

           Return a list of Ace::Sequence::Feature objects corresponding to coding sequence.  THIS IS NOT YET
           IMPLEMENTED.

       relative()
             $relative = $gene->relative;
             $gene->relative(1);

           This turns on and off relative coordinates.  By default, the exons and intron features will be
           returned in the coordinate system used by the gene.  If relative() is set to a true value, then
           coordinates will be expressed as relative to the start of the gene.  The first exon will (usually) be
           1.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList,
       GFF

AUTHOR

       Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

       Copyright (c) 1999, Lincoln D. Stein

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl
       itself.  See DISCLAIMER.txt for disclaimers of warranty.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 168:
           You forgot a '=back' before '=head1'