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rRNA gene sequence databases (metagenomic analysis)

Once OTUs are determined, it is necessary to determine from which species they came. For rRNA gene sequences several databases exist.

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RDP
Web
Desktop

RDP Ribosomal Database Project

Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along…

Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along with tools to allow researchers to analyse their own rRNA gene sequences. RDP offers tools for browsing and searching the…

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ARB
Desktop

ARB

Provides several tools for sequence database maintenance and analysis. ARB is a…

Provides several tools for sequence database maintenance and analysis. ARB is a graphically oriented package that consists of software tools directly interacting with one another as well as the…

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RNAmmer
Web

RNAmmer

Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

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5SRNAdb
Dataset

5SRNAdb 5S Ribosomal RNA Database

A database dedicated to nucleotide sequences of bacterial, archaeal and…

A database dedicated to nucleotide sequences of bacterial, archaeal and eukaryotic (cytoplasmic and organellar) 5S ribosomal RNAs and their genes. The sequences for particular organisms can be…

rrnDB
Dataset

rrnDB

A searchable database documenting variation in ribosomal RNA operons in…

A searchable database documenting variation in ribosomal RNA operons in Bacteria and Archaea. The redesigned rrnDB brings a substantial increase in the number of genomes described, improved curation,…

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SILVA
Dataset

SILVA

Provides up to date, quality-controlled databases of aligned ribosomal RNA…

Provides up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. silva contains 3…

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cpnDB
Dataset

cpnDB

A curated collection of chaperonin sequence data collected from public…

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology…

PR2 Database
Dataset

PR2 Database Protist Ribosomal reference database

Provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and…

Provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy.

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RPG
Dataset

RPG Ribosomal Protein Gene database

Compiles ribosomal protein (RP) genes from various species. RPG aims to improve…

Compiles ribosomal protein (RP) genes from various species. RPG aims to improve comparative studies of gene evolution. The database includes chromosomal positions, accession numbers, gene and CDS…

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Greengenes
Web

Greengenes

Provides quality-controlled microbial DNA data and tools to researchers for…

Provides quality-controlled microbial DNA data and tools to researchers for rapid analysis of user-generated sequences.

probeBase
Dataset

probeBase

A manually maintained and curated database of rRNA-targeted oligonucleotide…

A manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against…

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The Small…
Web

The Small Subunit rRNA Modification Database

Provides a listing of reported post-transcriptionally modified nucleosides and…

Provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya.

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PhytoREF
Dataset

PhytoREF

Explores, evaluates and monitors the diversity of photosynthetic eukaryotes in…

Explores, evaluates and monitors the diversity of photosynthetic eukaryotes in aquatic and terrestrial ecosystems. PhytoREF is a database built through the compilation of all of the publicly…

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FoodMicrobionet
Dataset

FoodMicrobionet

Permits to explore multiple datasets generated by 16S rRNA gene amplicon…

Permits to explore multiple datasets generated by 16S rRNA gene amplicon high-throughput sequencing (HTS) studies of food bacterial communities. FoodMicrobionet is a database and visualisation tool…

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Microcontax
Desktop

Microcontax

Contains designed data sets based on a consensus taxonomy assignment among…

Contains designed data sets based on a consensus taxonomy assignment among several data repositories. Microcontax is an R data package and a consensus taxonomy for prokaryotes designed to be the best…

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EzTaxon-e
Dataset

EzTaxon-e

Covers not only species within the formal nomenclatural system but also…

Covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature.

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SILVAngs
Web

SILVAngs

Allows data analysis of ribosomal RNA gene (rDNA) amplicon reads from…

Allows data analysis of ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing as next-generation sequencing (NGS) approaches. SILVAngs is a web interface which uses as a reference…

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the DARC site
Dataset

the DARC site The Database for Aligned Ribosomal Complexes site

Gathers information about Cryo-electron microscopy (cryo-EM) density maps and…

Gathers information about Cryo-electron microscopy (cryo-EM) density maps and atomic coordinates of ribosomal particles from Protein Data Bank (PDBs) and Electron Microscopy Data Bank (EMDB). Users…

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myPhyloDB
Desktop

myPhyloDB

A user-friendly personal database with a browser-interface designed to…

A user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files,…

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MetaMetaDB
Dataset

MetaMetaDB Meta- Metagenomic Data Base

Collects 16S rRNA sequences from a large number of datasets. MetaMetaDB is a…

Collects 16S rRNA sequences from a large number of datasets. MetaMetaDB is a comprehensive (‘‘meta-’’) and compact database that contains collection of 16S rRNA sequences associated with…

STPD
Dataset

STPD Salinity Tolerant Poplar Database

An integrative database for salt-tolerant poplar genome biology. Currently the…

An integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty…

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R-Syst::diatom
Dataset

R-Syst::diatom

An open-access and curated reference barcoding database for diatoms, developed…

An open-access and curated reference barcoding database for diatoms, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural…

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MiDAS
Dataset

MiDAS Microbial Database for Activated Sludge

Gathers information about the morphology, ecophysiology, abundance and…

Gathers information about the morphology, ecophysiology, abundance and distribution of genus members in full-scale treatment systems with phylotype identity. MiDAS was primarily a taxonomic database…

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FGR
Dataset

FGR Fungene Repository

Helps researchers to explore publicly available sequences harvested from…

Helps researchers to explore publicly available sequences harvested from GenBank and assigned to a specific collection of gene families. FGR employs a reference/model-based, comparative analysis…

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Renkan
Dataset

Renkan

Offers plankton symbiosis & Radiolaria database. The Renkan application is…

Offers plankton symbiosis & Radiolaria database. The Renkan application is used by the planktonic symbiosis research team at the Station Biologique de Roscoff to organize and share information on…

HOMD
Web

HOMD Human Oral Microbiome Database

A body site-specific public database providing the scientific community with…

A body site-specific public database providing the scientific community with comprehensive information on prokaryote species that are present in the human oral cavity. This dynamic database provides…

StaphyloBase
Dataset

StaphyloBase

Developed with the goal of having a one-stop genomic resource platform for the…

Developed with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic…

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RIM-DB
Dataset

RIM-DB Rumen and Intestinal Methanogen-DataBase

Supplies a collection of 16S rRNA gene sequences from ruminal methanogens and…

Supplies a collection of 16S rRNA gene sequences from ruminal methanogens and from various other intestinal environments where methanogens are known to be important hydrogen consumers. It is composed…

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