Cite as: Cold Spring Harb. Protoc.; 2010; doi:10.1101/pdb.prot5368

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protocolProtocol

Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes

Elizabeth M. Glass1, Jared Wilkening2, Andreas Wilke2,3, Dionysios Antonopoulos2,4,5, and Folker Meyer1,2,3

1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
2 Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
3 Computation Institute, University of Chicago, Chicago, IL 60637, USA
4 Biology Division, Argonne National Laboratory, Argonne, IL 60439, USA
5 Department of Medicine, University of Chicago, Chicago, IL 60637, USA

3Corresponding author (folker.meyer{at}gmail.com).


INTRODUCTION

Shotgun metagenomics creates millions of fragments of short DNA reads, which are meaningless unless analyzed appropriately. The Metagenomics RAST server (MG-RAST) is a web-based, open source system that offers a unique suite of tools for analyzing these data sets. After de-replication and quality control, fragments are mapped against a comprehensive nonredundant database (NR). Phylogenetic and metabolic reconstructions are computed from the set of hits against the NR. The resulting data are made available for browsing, download, and most importantly, comparison against a comprehensive collection of public metagenomes. A submitted metagenome is visible only to the user, unless the user makes it public or shares with other registered users. Public metagenomes are available to all.


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