NAME¶
Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript
SYNOPSIS¶
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
------------------------------------------------------------------------
DESCRIPTION¶
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.
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
BUGS¶
None reported.
SEE ALSO¶
Bio::DB::GFF, Bio::DB::GFF::Aggregator
AUTHOR¶
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.