Meta4 is a simple, flexible database system with a web-interface that allows the rapid sharing of metagenomic datasets with collaborators.

Starting with assembled and annotated contigs, bioinformaticians can create a Meta4 instance in less than an hour on most standard Apache web-servers.  The data can then be shared with collaborators over the web.

1. Code

The code is avialable at github.  The README includes instructions on how to set up a new instance.

2. Amazon Image

There is an AMI available, based on Ubuntu, running Apache2 with a Meta4 database including example data.  The current AMI is available in the EU-WEST region:

  • ami-46687f32 / Meta4

Information on how this was set up can be found here.

3. Example data

We have created an example Meta4 database and the results can be browsed at  Briefly, we downloaded data from Hess et al., 2011 (SRA accession SRA023560) and assembled the reads using SOAPdenovo.  Open-reading frames greater than 200bp in length were extracted as putative genes.  Pfam-A domains were annotated using 

As the experiment was designed to find novel biomass degrading genes, we en-courage users to enter “glyco_hydro” into the “Name” field and click “Submit”.

  1. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467

4. Feedback

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