Reference

Bio::DB::GFF::Aggregator::gene(3pm)

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 <[email protected]>.

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.

History