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EBI / EMBL-EBI - The European Bioinformatics Institute
Supplies an access to several biological data resources and bioinformatics services. EBI is a platform that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems, pathways, ontologies and literature. Databases, tools, as well as web services are provided for sharing data, performing queries and analyzing results. Users can also deposit their data through a data submission page. All the resources are freely available without restriction, with few exceptions.
IMG/VR
Visualizes and analyses viral sequences. IMG/VR allows users to explore associated metadata to decipher biogeographical and habitat distribution patterns of viral species as well as traveling across all the identified hosts putatively infected with viral sequences. Users can compare and analyze their sequences against IMG/VR’s data (including viral protein family models, viral cluster and singleton information, distribution patterns of similar viral sequences across the globe, percent of known and unknown genes per sequence, and information regarding viral taxonomy and putative viral-host(s)), integrated with a variety of analytical tools.
MetaBioME / Metagenomic BioMining Engine
A web resource to find novel homologs for known commercially useful enzymes (CUEs) in metagenomic datasets and completed bacterial genomes. MetaBioME can be used as an intuitive search engine to access manually curated data on the CUEs, stored in a relational database, along with several options to identify their homologues from multiple metagenomic datasets and completed bacterial genomes. Using MetaBioME, we have identified several novel homologues to known CUEs that can potentially serve as leads for further experimental verification.
HPMCD / Human Pan-Microbe Communities Database
Provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21,000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation.
MarDB
Includes all in-complete sequenced marine prokaryotic genomes regardless level of completeness. MarDB is a contextual and sequence part of MAR databases. This resource was built by compiling data from a number of publicly available sequence, taxonomy and literature databases in a semiautomatic fashion. There are three environmental metadata fields used for describing the sampling site of a microorganism in MarDB: environmental biome, feature and material which are controlled by a total of 95 terms.
The MAR databases
Provides a collection of databases that contains manually curated metadata. The MAR databases integrates attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information and their corresponding nucleotide and protein sequences. The set is composed of three contextual databases (MarRef, MarDB, MarCat) that are built in a semi-automatic way. They combine data from a number of publicly available sequence, taxonomy and literature.
iVirus
Leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes.
DIGAP / Database of Improved Gene Annotation for Phytopathogens
Provides annotations for the sequenced bacterial phytopathogen genomes. DIGAP is supported with a user-friendly designed web interface allowing users to search by gene name, DIGAP_ID, PID and gene function. Users can also query nucleotide or protein sequences, and the BLAST generates a list of hits which are organized according to the sequence identity between query and object sequences. The database allows understanding of lifestyle, metabolism and pathogenicity of some bacterial plant pathogens at molecular level.
BaMBa / Brazilian Marine Biodiversity
Allows integrated views of different data types concerning Brazilian marine environment. Essentially, any environmental information can be added to BaMBa. Certified datasets obtained from integrated holistic studies, comprising physical-chemical parameters, -omics, microbiology, benthic and fish surveys can be deposited in the new database, enabling scientific, industrial and governmental policies and actions to be undertaken on marine resources. There is a significant number of databases, however BaMBa is the only integrated database resource both supported by a government initiative and exclusive for marine data.
MetaRef
Obsolete
A resource to comprehensively catalog and characterize clade-specific microbial genes. MetaRef organizes currently available draft and finished bacterial and archaeal genomes into quality-controlled clades, reports all core and pan gene families at multiple levels in the resulting taxonomy, and it annotates families' conservation, phylogeny and consensus functional information. MetaRef also provides a comprehensive non-redundant reference gene catalogue for metagenomic studies, including the abundance and prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Project.
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