Bio::DB::GFF::Aggregator::so_transcript(3) Sequence Ontology Transcript


use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['so_transcript'],
Aggregator method: processed_transcript
Main method: mRNA
Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR


Bio::DB::GFF::Aggregator::so_transcript is identical to the processed_transcript aggregator, which was designed to be compatible with the Sequence Ontology canonical gene. 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.

The processed_transcript aggregator is loaded by default, so this is only needed for backward compatibility.


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


 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


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


None reported.


Lincoln Stein <[email protected]>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

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