Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.
By Elizabeth M. Glass, Jared Wilkening, Andreas Wilke, Dionysios A. Antonopoulos, Folker Meyer. Cold Spring Harbor Protocols, 2010
304 citations recorded by the source corpus.
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.
Subfields: Aerospace Engineering, Control and Systems Engineering, Fluid Flow and Transfer Processes
View Paper: https://www.semanticscholar.org/paper/88367e53821a9c1d0b946f74ac3b9a1e934e0190
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In Control and Systems Engineering
Citations in the corpus
- Metagenomics - a guide from sampling to data analysis (2012, methodology): “Some approaches, e.g. IMG/M, prefer assembled contigs, other pipelines such as MG-RAST [43] require only 75 bp or longer for gene prediction or similarity analysis that provides taxonomic binning and functional classification.”
- MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data (2016, methodology): “Services such as MG-RAST [21] and the EBI metagenomic web service [13] allow users to upload their data so as to use provided computational facilities for taxonomic and functional analysis of metagenomic sequencing data.”
- Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils (2014, methodology): “Shotgun metagenome reads were annotated in MG-RAST (Glass et al., 2010).”
- The Placenta Harbors a Unique Microbiome (2014, methodology): “E. M. Glass, J. Wilkening, A. Wilke, D. Antonopoulos, F. Meyer, Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.”
- In-feed antibiotic effects on the swine intestinal microbiome (2012, methodology): “Metagenome sequences (1,202,058 total) were analyzed in MG-RAST for SEED subsystems (26), and in-house for clusters of orthologous groups (COGs).”
- Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression (2014, methodology): “The data from Caporaso et al [3] were obtained from the MGRAST database [23] in a preprocessed form; i.”
- MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014, background): “On the other hand, homology-based approaches such as those employing BLAST (17) and HMMER3 (18) searches of assembled or unassembled sequences against known reference database(s), have become a nearly indispensible component of metagenomic studies (4).”