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| Version | Summary | Created by | Modification | Content Size | Created at | Operation |
|---|---|---|---|---|---|---|
| 1 | Sirius Huang | -- | 1169 | 2022-10-10 01:43:32 |
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MG-RAST is an open-source web application server that suggests automatic phylogenetic and functional analysis of metagenomes. It is also one of the biggest repositories for metagenomic data. The name is an abbreviation of Metagenomic Rapid Annotations using Subsystems Technology. The pipeline automatically produces functional assignments to the sequences that belong to the metagenome by performing sequence comparisons to databases in both nucleotide and amino-acid levels. The applications supplies phylogenetic and functional assignments of the metagenome being analysed, as well as tools for comparing different metagenomes. It also provides a RESTful API for programmatic access. The server was created and maintained by Argonne National Laboratory from the University of Chicago. In December 29 of 2016, the system had analyzed 60 terabase-pairs of data from more than 150,000 data sets. Among the analyzed data sets, more than 23,000 are available to the public. Currently, the computational resources are provided by the DOE Magellan cloud at Argonne National Laboratory, Amazon EC2 Web services, and a number of traditional clusters.
References
- Meyer, F.; Paarmann, D.; D'Souza, M.; Olson, R.; Glass, EM; Kubal, M.; Paczian, T.; Rodriguez, A. et al. (2008-01-01). "The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes". BMC Bioinformatics 9: 386. doi:10.1186/1471-2105-9-386. ISSN 1471-2105. PMID 18803844. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2563014
- Angiuoli, Samuel V.; Matalka, Malcolm; Gussman, Aaron; Galens, Kevin; Vangala, Mahesh; Riley, David R.; Arze, Cesar; White, James R. et al. (2011-01-01). "CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing". BMC Bioinformatics 12: 356. doi:10.1186/1471-2105-12-356. ISSN 1471-2105. PMID 21878105. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3228541
- Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy; Cole, James R.; Dawyndt, Peter; Garrity, George M.; Gilbert, Jack; Glöckner, Frank Oliver et al. (2011-06-21). "The Genomic Standards Consortium". PLOS Biology 9 (6): e1001088. doi:10.1371/journal.pbio.1001088. ISSN 1545-7885. PMID 21713030. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3119656
- Keegan, Kevin P.; Glass, Elizabeth M.; Meyer, Folker (2016-01-01). MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. 1399. 207–233. doi:10.1007/978-1-4939-3369-3_13. ISBN 978-1-4939-3367-9. https://dx.doi.org/10.1007%2F978-1-4939-3369-3_13
- Wilke, Andreas; Harrison, Travis; Wilkening, Jared; Field, Dawn; Glass, Elizabeth M.; Kyrpides, Nikos; Mavrommatis, Konstantinos; Meyer, Folker (2012-01-01). "The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools". BMC Bioinformatics 13: 141. doi:10.1186/1471-2105-13-141. ISSN 1471-2105. PMID 22720753. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3410781
