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Manual Reference Pages  -  BIO::DB::GFF::AGGREGATOR::SO_TRANSCRIPT (3)

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NAME

Bio::DB::GFF::Aggregator::so_transcript -- Sequence Ontology Transcript

CONTENTS

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.

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perl v5.20.3 BIO::DB::GFF::AGGREGATOR::SO_TRANSCRIPT (3) 2016-04-05

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