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.