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Bio::DB::GFF::Aggregator::gene.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::GFF::Aggregator::gene -- Sequence Ontology GeeneSYNOPSIS
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::AggregatorAUTHOR
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre