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RDP / Ribosomal Database Project
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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 data collections, for taxonomic classification and nearest neighbour 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.
Microcontax
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 possible for training taxonomic classifiers based on 16S rRNA sequence data. It offers functions for looking up higher-level taxonomy of specified genera. It also implements some ways to express uncertainties in the classifications, indicating if the input sequences are difficult to recognize.
HOMD / Human Oral Microbiome Database
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 a curated taxonomy of oral prokaryotes, a curated set of full-length 16S rRNA reference sequences, and BLAST tools that allow the identification of unknown isolates or clones based on their 16S rRNA sequence; additionally, phenotypic, bibliographic, clinical and genomic information are linked for each taxa. The web-based interfaces and software tools are implemented to facilitate the query and analysis of this comprehensive dataset.
myPhyloDB
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, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g., ANOVA, t-tests, linear regression, DESeq2, and PCoA) and normalization (rarefaction, DESeq2, proportion) tools for the comparative analysis of taxonomic abundance, species richness, and species diversity for projects of various types (e.g., human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired.
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probeBase
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.
5SRNAdb / 5S Ribosomal RNA Database
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.
the DARC site / The Database for Aligned Ribosomal Complexes site
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
PhytoREF
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.
MiDAS / Microbial Database for Activated Sludge
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.
FGR / Fungene Repository
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.
R-Syst::diatom
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.
FoodMicrobionet
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.
MetaMetaDB / Meta- Metagenomic Data Base
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’’.
STPD / Salinity Tolerant Poplar Database
Obsolete
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 habitats, has become a valuable genetic resource for the exploitation of tolerance characteristics in trees. This database contains curated data including genomic sequence, genes and gene functional information, non-coding RNA sequences, transposable elements, simple sequence repeats and single nucleotide polymorphisms information of P. euphratica, gene expression data between P. euphratica and Populus tomentosa, and whole-genome alignments between Populus trichocarpa, P. euphratica and Salix suchowensis. The STPD provides useful searching and data mining tools, including GBrowse genome browser, BLAST servers and genome alignments viewer, which can be used to browse genome regions, identify similar sequences and visualize genome alignments. Datasets within the STPD can also be downloaded to perform local searches.
RIM-DB / Rumen and Intestinal Methanogen-DataBase
Obsolete
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 of primarily sequences longer than 1,200 bp that cover large parts of the almost 1,540 bp long gene. The database includes shorter sequences if they originated from isolates or enrichment cultures. It is suitable for the analysis of amplicon data that have been generated for variable regions other than the V6–V8 region.
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