Tag: metagenomics

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the gene ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data th ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing ...

Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here we present the 3rd version of IMG/VR, composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), n ...

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughou ...

For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel ge ...

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.

The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and in ...

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organization—from the genome to ...

The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems. Effective bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, eu ...

The Eukaryotic Ribosomal Internal Transcribed Spacer 1 Database (ITSoneDB) is a collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. It is intended to provide a curated reference database aimed at ITS1-based metageno ...

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

tRNA Gene DataBase Curated by Experts

Prokaryotic 2-Component Systems database

a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. gutMDisorder (http: bio-annotation.cn gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbi ...

Prediction of intact secretion systems III, IV and VI in bacterial genomes by using a Support Vector Machine (SVM) approach.

proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. ...

CDISC Glossary seeks to harmonize definitions (including acronyms, abbreviations, and initials) used in the various standards initiatives undertaken by CDISC in clinical research. Glossary also serves the community of clinical researchers by selectin ...

COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile. By tracking unique id ...

a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. MEGAResFrom MEG, the Microbial Ecology Group. Welcome to MEGARes: an Antimicrobial Database for High-Throughput Sequencing. ...

Metagenomic BioMining Engine: homologs of commercially useful enzymes in metagenomic datasets

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene ...

a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and acce ...

Experimentally characterized CAZyme gene clusters

WDCM 10K sequencing projects

MarCat is a gene (protein) catalogue of uncultivable and cultivable marine microorganisms derived from metagenomics samples.

Database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB) ...

A comprehensive database for target genes of gut microbes and microbial metabolites.

Human metagenomic extrachromosomal mobile genetic elements

Curated and standardized metadata for human metagenomes

Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database

AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis.

A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated meta ...

Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples.

Database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space.

Taking advantage of a decade of Daphnia '-omics' data for gene annotation | Welcome to the Daphnia Stressor database

Advancing a comprehensive database of bacterial plasmids.

AciDB is a database of about 600 manually curated acidophilic organisms, their genomic information and associated metadata.

A curated database for microbes across human body and their associations with health and diseases.

A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a peri ...

A portal for geographic reference data for the Amazon.

dbPUP is a database of polyphenol utilization proteins (PUPs) that have been experimentally characterized to metabolize polyphenol substrates.

AncientMetagenomeDir is a community curated resource of metadata of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples

Construct full-length, horizontally acquired Antibiotic Resistance Genes (ARGs) from sequencing datasets. It has been designed with environmental metagenomics and microbiome experiments in mind, where the diversity and relative abundance of ARGs need ...

A database of microorganisms and proteins linked to plastic biodegradation.

Database and Tool for Metataxonomics with Long-Read Sequence.

A comprehensive database for profiling prokaryotic pan-genome dynamics.

A standardized database to study deep sequenced metagenomic data from human fecal specimen.

Statistical detection of pathogen-associated protein domains.

A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

Mine bacterial (meta-)genomic DNA for bacteriocins and RiPPs. Additionally it provides databases and a BLAST against the core peptide databases.

MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.

The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and sta ...

A Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.

Phylogenize is a web tool that allows users to link microbial genes to environments, accounting for phylogeny. More specifically, given community composition data, phylogenize links genes in microbial genomes to either microbial prevalence in, or sp ...

metaXplor is an interactive viral and microbial metagenomic data manager. It aims at storing large volumes of user-defined sample, sequence and assignment information while providing a user-friendly fine-filtering web-interface. This online GUI also ...

Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons.

BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use ...

Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequen ...

CBS offers Comprehensive public databases of DNA- and protein sequences, macromolecular structure, g ene and protein expression levels, pathway organization and cell signalling, have been established to optimise scientific exploitation of the explosi ...