Bio::DB::GFF::Aggregator::processed_transcript(3pm) | User Contributed Perl Documentation | Bio::DB::GFF::Aggregator::processed_transcript(3pm) |
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 exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR ------------------------------------------------------------------------
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 "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.
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.
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.
2020-01-13 | perl v5.30.0 |