---
name: "Bio::DB::GFF::Aggregator::gene"
section: "3pm"
platform: "linux"
package: "libbio-db-gff-perl"
version: "1.7.4-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::DB::GFF::Aggregator::gene"
---

# Bio::DB::GFF::Aggregator::gene(3pm)

## NAME

Bio::DB::GFF::Aggregator::gene -- Sequence Ontology Geene

## SYNOPSIS

```
  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::Aggregator

## AUTHOR

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.