The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-09-19

AUTHORS

F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards

ABSTRACT

BackgroundRandom community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.ResultsA high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats.ConclusionThe open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data.http://metagenomics.nmpdr.org More... »

PAGES

386

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-9-386

DOI

http://dx.doi.org/10.1186/1471-2105-9-386

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006083026

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18803844


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72 metagenomics RAST
73 metagenomics RAST server
74 microbes
75 multiple data sources
76 multiple users
77 new paradigm
78 next-generation sequencing
79 nucleotide database
80 paradigm
81 pipeline
82 primary bottleneck
83 privacy
84 protein
85 public resources
86 range
87 researchers
88 resources
89 sequence
90 sequence analysis
91 sequencing
92 server
93 services
94 source
95 standard view
96 summary
97 support
98 tool
99 types
100 user access
101 users
102 variety
103 variety of formats
104 view
105 wide range
106 years
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