Meta4

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 http://www.ark-genomics.org/tools/meta4.  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 pfam_scan.pl. 

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

Feedback should be sent to mick.watson@roslin.ed.ac.uk