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Microbial community databases | Comparative genomics

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil,…
EBI
Dataset

EBI EMBL-EBI - The European Bioinformatics Institute

Supplies an access to several biological data resources. EBI is a database that…

Supplies an access to several biological data resources. EBI is a database that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems,…

IMG/VR
Dataset

IMG/VR

Visualizes and analyses viral sequences. IMG/VR allows users to explore…

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…

iVirus
Dataset

iVirus

Leverages the CyVerse cyberinfrastructure to provide access to viromic tools…

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…

EBI…
Dataset

EBI metagenomics

A freely available hub for the analysis and archiving of metagenomic and…

A freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. EBI metagenomics allows users to easily submit raw nucleotide reads for functional and taxonomic…

MG-RAST
Dataset

MG-RAST

An open-submission data portal for processing, analyzing, sharing and…

An open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of…

HPMCD
Dataset

HPMCD Human Pan-Microbe Communities Database

Provides a manually curated, searchable, metagenomic resource to facilitate…

Provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. The HPMC database provides species level, standardized phylogenetic…

Phamerator
Desktop

Phamerator

Analyzes and represents phage genome mosaicism. Phamerator performs pair wise…

Analyzes and represents phage genome mosaicism. Phamerator performs pair wise similarity searches between predicted protein products of a set of phage genomes. Results can be displayed as genome maps…

MetaRef
Dataset

MetaRef

A resource to comprehensively catalog and characterize clade-specific microbial…

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…

MicrobiomeAnaly…
Web

MicrobiomeAnalyst

Integrates recent progress in statistics and visualization techniques.…

Integrates recent progress in statistics and visualization techniques. MicrobiomeAnalyst provides an analysis of common data outputs produced from microbiome studies. It gives support for diversity…

MetaBioME
Dataset

MetaBioME Metagenomic BioMining Engine

A web resource to find novel homologs for known commercially useful enzymes…

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…

Abasy Atlas
Dataset

Abasy Atlas Across-bacteria systems Atlas

Provides a comprehensive atlas of annotated functional systems, global network…

Provides a comprehensive atlas of annotated functional systems, global network properties and systems-level elements. Abasy Atlas provides data enabling large-scale comparative systems biology…

DIGAP
Dataset

DIGAP Database of Improved Gene Annotation for Phytopathogens

Provides annotations for the sequenced bacterial phytopathogen genomes. DIGAP…

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…

BaMBa
Dataset

BaMBa Brazilian Marine Biodiversity

Allows integrated views of different data types concerning Brazilian marine…

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…

IntegromeDB
Dataset

IntegromeDB

A biological web search engine based on the Semantic Web technologies. The…

A biological web search engine based on the Semantic Web technologies. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways,…

iMicrobe
Dataset

iMicrobe

Enables discovery and access to microbial datasets consisting of project…

Enables discovery and access to microbial datasets consisting of project information, omics data and assemblies, metadata, and other associated files. Data in the iMicrobe Data Commons can be used in…

Comprehensive…
Dataset

Comprehensive Microbial Resource

Compiles information about sequence and annotation for complete and publicly…

Compiles information about sequence and annotation for complete and publicly available bacterial and archaeal genomes. CMR can be used as a resource to perform retrievals pertaining to inter and…

GenoMycDB
Dataset

GenoMycDB

Gathers data about whole sequenced mycobacterial genomes. GenoMycDB aims to…

Gathers data about whole sequenced mycobacterial genomes. GenoMycDB aims to furnish a repository for allowing large-scale comparative analysis according to their predicted protein content. The…

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