Bio::DB::GFF::Aggregator::processed_transcript -- 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 => ['processed_transcript'], ); ------------------------------------------------------------------------ Aggregator method: processed_transcript Main method: mRNA Sub methods: CDS 5'-UTR 3'-UTR transcription_start_site polyA_site ------------------------------------------------------------------------ Bio::DB::GFF::Aggregator::processed_transcript is one of the default aggregators, and was written to be compatible with the Sequence Ontology canonical gene. It aggregates raw "CDS", "5'-UTR", "3'-UTR", "transcription_start_site" and "polyA_site" features into "gene" features. The UTRs may also be named "untranslated_region," "five_prime_untranslated_region," or "three_prime_untranslated_region."

method
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "processed_transcript" 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 None reported. Bio::DB::GFF, Bio::DB::GFF::Aggregator Lincoln Stein <lstein@cshl.org>. 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.