Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data source, along with tools to allow researchers to analyze their own rRNA gene sequences. RDP offers tools for browsing and searching the data collections, for taxonomic classification and nearest neighbor search, for primer-probe testing and for tree building. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics.
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 the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.
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 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Its Browser implements a hierarchical view on the database contents, similar to a file browser, visualizing any of the taxonomies included with SILVA.
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 retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. All data that have been used to create the database can be downloaded from the web page and from interactive windows, and can be used in subsequent data-mining applications.
Provides data and analytics portal focuses on taxonomy, ecology, genomics and metagenomics. EZioCloud is an integrated database with a complete taxonomic hierarchy of the Bacteria and Archaea represented by 16S rRNA gene and genome sequences. All genomes were identified taxonomically at the kind, species or subspecies levels using a combination of gene-based search.
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 studies.
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, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing.
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 sizes, orthologs, snoRNAs and links to other public databases. Each record is linked to an orthologous gene classification table, except for human which are related to a gene table or a chromosomal map position.
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 can make searches by EMDB or PDB accession number (ID) or use the drop-down menu to restrict the search to Source Database or ID, title, author, abstract or PubMed ID, as well as method, organism, ligand, classification or particle type
Collects ribosomal DNA sequences from cultured isolates and morphologically identified organisms with taxonomy of different eukaryotic lineages. EukRef intends to assemble a curated reference database of 18S rRNA gene sequences covering all eukaryotes. This repository arranges and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. It exploits the GenBank accession numbers for the sequences to retrieve the classification string and relevant metadata from GenBank.
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 available plastidial 16S rDNA sequences (amplicons and sequences extracted from plastidial genomes), as well as novel Sanger amplicons. This database could also facilitate the development of a range of applications in biomonitoring photosynthetic eukaryotes in various habitats, palaeoecological studies of primary producers in past environments and dietary studies in unicellular and multicellular herbivores.
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 Research). R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). In addition to these information, morphological features (e.g. biovolumes, chloroplasts...), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom.
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 curated for abundant and process important phylotypes for activated sludge wastewater treatment systems with biological nutrient removal. The repository also includes the organisms of the anaerobic digestion community and the most abundant influent wastewater organisms.
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 strategy to build the reference database and helps to study functional and phylogenetic diversities of specific gene families. This strategy relies on the use of HMMER3 and Hidden Markov Models (HMM). The FGR currently contains 77 gene families organized into seven categories: Antibiotic resistance, Biodegradation, Biogeochemical Cycles, Metal Cycling, Phylogenetic Markers, Plant Pathogenicity, and “Other” for gene families not in the listed categories.
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 diverse environments. Users can submit the 16S rRNA sequences of certain prokaryotes and thus can investigate the microbial habitability for analyzing the ecology and evolution of prokaryotes. The database provides a reverse perspective of the environments in which each prokaryotic group exists, opening the door to the investigation of ‘‘meta-metagenomics’’.
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 based on network analysis. This online resource can also be used to obtain further information on distribution of taxa in different food groups by filtering and recalculation from nodes and edges tables. It allows researchers in the food microbiology to benefit from the significant advances that HTS is providing in this key field of research.
Allows users to detect contaminated prokaryotic genomes. ContEst16S is an online repository that permits researchers to consult information about contaminated genomes. In this database, 16S rRNA gene fragments from the query genome assemblies are screened to see if the genome assembly is contaminated or not. Its online interface notably provides access to several Genbank data.
Provides a manually curated repository for taxonomy annotation of 16S ribosomal RNA (rRNA) gene sequences from bacterial species of dairy products. DAIRYdb includes more than 10 000 complete sequences of 16S from dairy products with a taxonomy organized on 7 ranks. It intends to reduce conflicting miss-annotated sequences and manual curation while covering inspected biodiversity. This database can be integrated in any classification prediction tool.
Describes information linked to oral microbe species. HOMD is a body site-specific public database that provides the scientific community with information on prokaryote species which are present in the human oral cavity. The database also includes BLAST tools for identifying unknown isolates or clones based on their 16S rRNA sequence, as well as phenotypic, bibliographic, clinical and genomic information for each taxa. It can serve as a model for microbiome data from other human body sites.