There are two types of searches available in MG-RAST

1) simple searches  – simple text query applied against multiple database fields
2) advanced searches  – specify complex boolean queries combining multiple database fields

Both types of queries return a list of samples that match the query criteria.

We present a series of  examples for searches:

Example 1: Search metadata  for “fish gut”.

Example 2: Search for metagenomes annotated with “Lysine biosynthesis”.

Example 3: Complex search combining multiple fields

Use the advanced search dialog to find samples with “Biome equals freshwater” and “Country is United States“

The first drop down menu provide a list of the main categories to search, we picked: Metadata.

Once selected, the system will display the metadata fields that can be searched.

Here we picked the Biome and a new list of controlled terms for this metadata field opens up:

After selecting “freshwater”, multiple other categories can be added by pressing the (+) sign.

Since we use the combined M5NR for our sequence similarity searches and assign terms from multiple namespaces (e.g. COG, KEGG, SEED Subsystems etc) at the same time.

Search for metagenomes annotated with specific functional classification terms.

Below we show the search for SEED subsystem category DNA metabolism. The system will provide a list of the controlled vocabulary terms.

The user has to specify which functional namespace to search:

Search for metagenomes annotated with specific functional terms.

You can also search for specific functions, however note that searching for e.g. Kinase will return an error since the number of results is astronomical. Try a more specific search: find metagenomes with genes annotated as fructokinase that are classified as fossil (Biome).

View metagenome results mapped via longitude and latitude metadata.

Click on ‘map metagenomes’ below:

And see the following mapped locations below.  Click on a red tag to see details on the metagenomes at that location.