Downloading 16S sequences using JGI portal

As an example, consider a query to retrieve all 16S rRNA genes longer
than 500nt in the freshwater sediment metagenomes in IMG. First a user
would identify all freshwater sediment metagenomes in IMG, which can
be done using the Advanced Search Builder in Genome Search and the
following query conditions:

Taxonomy – Domain: *Microbiome

Study Dataset Names – Genome Name / Sample Name: Freshwater

Environmental Classification – GOLD Ecosystem Type: Sediment

This Genome Search query retrieves a total of 22 metagenomes, which
can be selected and added to the Genome Cart. In order to find all 16S
rRNA genes longer than 500nt in these metagenomes a user would go to
the Advanced Search Builder in the Gene Search interface and add the
following query conditions (Figure 2A):

Gene Model Attributes – Locus Type: rRNA_16S

Gene Statistics – Gene Amino Acid Length: > 500

and add all metagenomes in the Genome Cart to the set of ‘Selected
Genomes.’ The query retrieves 131 16S rRNA genes (Figure 2B), which
can be selected and added to Gene Cart for further analysis. Gene Cart
also allows exporting selected gene sequences in a FASTA format.
Similar to the Genome Search interface, Gene Search also records all
search history to allow users to view and to reuse their previous
queries (Figure 2C).