NAME

Bio::DB::GFF::Aggregator::so_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 => ['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
------------------------------------------------------------------------
            
          

DESCRIPTION

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.

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.