NAME

Bio::DB::GFF::Aggregator::gene -- Sequence Ontology Geene

SYNOPSIS

  use Bio::DB::GFF;

  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
				   -aggregator => ['gene'],
				 );

 ------------------------------------------------------------------------
 Aggregator method: gene
 Main method:       mRNA
 Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site
 ------------------------------------------------------------------------

DESCRIPTION

Bio::DB::GFF::Aggregator::gene is identical to so_transcript, but is used in those cases where you would like the name of the aggregated feature to be "gene" rather than "processed_transcript". It aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features into "mRNA" features. The UTRs may also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region,", "5'-UTR," and other synonyms.

method

Title   : method
Usage   : $aggregator->method
Function: return the method for the composite object
Returns : the string "gene"
Args    : none
Status  : Public

part_names

Title   : part_names
Usage   : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
Args    : none
Status  : Public

main_name

Title   : main_name
Usage   : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args    : none
Status  : Public

BUGS

None reported.

SEE ALSO

Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2008 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.