The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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Summary
The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
- Type
- article
- Published
- 2012-11-27
- Cited by
- 29,140
- References
- 25
- Access
- Open access
- OpenAlex
- https://openalex.org/W2034285706
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9696817
Keywords
Biology, Ribosomal RNA, Upload, Gene, Computational biology
References
- Megx.net: integrated database resource for marine ecological genomics
- Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
- Release LTPs104 of the All-Species Living Tree.
- probeBase—an online resource for rRNA-targeted oligonucleotide probes: new features 2007
- RNAmmer: consistent and rapid annotation of ribosomal RNA genes
- Archaeal Diversity in Waters from Deep South African Gold Mines
- Novel lineages of Planctomycetes densely colonize the alkaline gut of soil-feeding termites (Cubitermes spp.).
- QIIME allows analysis of high-throughput community sequencing data
- Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time‐series Study site
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
- SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
- Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources
- List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet.
- The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- ARB: a software environment for sequence data.
- The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
- The International Nucleotide Sequence Database Collaboration
- The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
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