Tag: model organisms

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear ...

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...

The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

Yeast GFP fusion localization database.

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

TriTrypDB is one of the databases that can be accessed through the VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these ...

HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) an ...

Detects this family of direct repeats found in the DNA of many bacteria and archaea.

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which informatio ...

The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, enviro ...

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, anal ...

IMGT/3Dstructure-DB (1,2) is the three-dimensional (3D) structure database of IMGT®, the international ImMunoGenetics information system® (3,4) that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT ...

CAMPR3 (Collection of Anti-Microbial Peptides) has been generated to enhance research into AMP families. The collection is compatible with well-known databases such as PubMed and Uniprot with information like sequence, protein definition, accession n ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).

MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned ...

The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology term ...

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...

Online GEne Essentiality database

Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.

The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty St ...

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.

The European Mouse Mutant Archive (EMMA) is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. The laboratory mouse is the most important m ...

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of ge ...

GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed ...

A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.

The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.

A suite of Web-based tools for comparative genomics

Tool for visualising the syntenic context of any gene from several yeast genomes.

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D br ...

The Hymenoptera Genome Database (HGD) is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD is divided into three main divisions: BeeBase, which hosts bee genomes and the Bee Pes ...

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas an ...

A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database ...

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

The Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.

This database summarizes our knowledge of replication origins in the budding yeast Saccharomyces cerevisiae. Each proposed origin site has been assigned a Status (Confirmed, Likely, or Dubious) expressing the confidence that the site genuinely corres ...

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

PRGdb is an open and daily updated space about plant resistance genes, in which all information about this family is stored, curated and discussed. This resource encourages research community curation of plant resistance genes.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life.

Collaborative resource for the Bacillus community.

Genome database of the beetle Tribolium castaneum

VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.

The ApiDB website (http://eupathdb.org/eupathdb) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center that integrates numerous database resources. The phylum Apicomplexa comprises numerous veterinary and med ...

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 ...

A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL) p ...

CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology pr ...

The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the ST ...

Knowledge base integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation, bibliography, structural views and comparative genomics, in a structured manner required for the rational development of new dia ...

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tis ...

A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive ann ...

The platform enables biologists to examine a gene, protein, compound or disease of interest in a global, biological, or clinical context.

The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musc ...

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog ...

Rice transcriptome under natural conditions

Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery o ...

Polymorphic miRNA-mediated gene regulation in vertebrates

GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtracti ...

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...

A comprehensive online knowledgebase for the monkey research community.

To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predic ...

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are impo ...

The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more th ...

ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The data ...

This tool is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-databas ...

PeroxiRedoxin classification indEX

Predicted proteins from C. elegans

EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and m ...

euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, ...

circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-dept ...

The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database fo ...

Protective antigen database and analysis system

Legionella pneumophila genome database.

Predicted Arabidopsis Interactome Resource

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 ...

Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including au ...

DNA repair pathways of human, yeast and E.coli

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that p ...

CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biologic ...

High-throughput screening using the CRISPR/Cas-9 system

The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information o ...

Structural data within the Immune Epitope Database

Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family class ...

Sequence, structure, and other data on pathogen antigens

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...

The datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helic ...

The MMRRC distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community. The Catalog provides information on the strains ava ...

IsoRank PPI Network Alignment Based Ortholog Database

Wiki for coordinating nematode sequencing projects

ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...

Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2

Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super ...

Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA ...

Wiki database of biological databases

Initiated in 2013, DMDD has the ambitious goal of identifying all embryonic lethal knockout lines made at the Wellcome Trust Sanger institute, through their work as a major centre for creation of individual mouse gene knockouts. DMDD uses a combinati ...

EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...

The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.

Genome-WIde Docking Database: 3D structures of protein complexes

It is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 spec ...

GWAS prioritization tool

Contains high- and low-throughput data relevant to phosphorylation events. It includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments.

Mutant mouse lines held at MRC Harwell

Integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Sacc ...

Comparative genomics of Fusarium strains

WDCM 10K sequencing projects

Experimentally characterized Prokaryotic GlycoProteins

A database of eukaryotic sequencing projects

Integrated database of mammalian genomes, phenotypes, strains and cell lines

A database for systems biology of DNA dynamics during the cell life.

A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic ...

ClinEpiDB is an open-access online resource for clinical and epidemiologic studies. The website allows users to visualize and subset data directly in the ClinEpiDB browser and explore potential associations. Supporting study documentation aids contex ...

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel images of proteomes from organisms with known genome information (available at http://gelbank.anl.gov). GELBANK serves as a database for those proteomics labs t ...

Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available.

an interactive database of human snoRNA sequences, abundance and interactions. Tool to visualize expression data in heatmaps. Column Options Reset Filters Refresh Table. snoTHAW is a tool to help visualize snoRNA expression data from snoDB

Voltage-gated potassium channel database

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play ...

MIPS mouse functional genomics database

PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation and the portal has a broad sci ...

The MUGEN mouse database (MMdb) is a database of murine models of immune processes and immunological diseases.

Interacting and non-interacting protein pairs

Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.

A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vert ...

Assembled partial genomes for ~250 eukaryotic organisms

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

It is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying database ...

dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea).

Protein stability data

The Canadian Rare Diseases Models and Mechanisms (RDMM) Network. Japanese Rare Disease Models & Mechanisms Network.

A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.

Phylogenetic Exploration of Viruses and their Evolutionary Relationships

The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed ...

Online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with ...

PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...

Alternative splicing during development in 20 species

anti-CRISPR operons

Microbial genome and functional analysis of Bacillus subtilis.

EPSD (Eukaryotic Phosphorylation Sites Database) is a well-annotated data resource of protein phosphorylation sites in eukaryotes.

The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) is a database of barcoded Chytridiomyceta and Blastocladiomycota cultures.

Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis

Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

Conserved Unique Peptide Patterns (CUPP) is a approach for sequence analysis employing conserved peptide patterns for determination of similarities between proteins. CUPP performs unsupervised clustering of proteins for formation of protein groups an ...

A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacteria ...

A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Su ...

A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.

An online database towards comprehensive essential gene annotation for prokaryotes.

Versatile databases for genomic sequencing and lab management. LabxDB comes with ready-to-use databases. Data is stored in PostgreSQL. LabxDB provides web-browser GUI and a programmatic API for intregration into pipelines. LabxDB for high-throughpu ...

KAIKObase is a silkworm genome database.

A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via ...

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

Leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

A comprehensive database for decoding the regulatory transcription co-factors in human and mouse.

YEASTRACT+ combines the existing database information of all yeast species, providing bioinformatics tools for the prediction and visualization of gene and genomic regulation based on orthologous regulatory associations described for other yeast spec ...

An informational platform for genome biology of grass carp. Grass carp (Ctenopharyngodon idellus) is a herbivorous, freshwater fish species of the family Cyprinidae, and the only species of the genus Ctenopharyngodon.

scAPAdb provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level in six species based on a large volume of scRNA-seq data. Currently, scAPAdb records APA information in animal speci ...

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 ...

Model organism database for the bacterium Myxococcus xanthus.

A portal for geographic reference data for the Amazon.

The site-symmetry induced representations of layer groups on the Bilbao Crystallographic Server.

Sequence composition dynamics of genes and genomes.

The database of zoonotic and vector-borne viruses.

CoFly is a gene coexpression database for the fruit fly Drosophila melanogaster

A comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species.

Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.

A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases.

CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species.

DeepMitoDB is a database of experimental and predicted subcellular localization of mitochondrial proteins with exteded functional annotation.

Is an online platform focuses on providing an up-to-date account of Botryosphaeriales with notes on orders, families and genera and species, keeping abreast of the current literature.

Expansin Engineering Database integrates information on sequence, structure and function of expansins.

A database of organ-specific metastasis induced by human cancer cell lines in mouse models. The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metas ...

A database for alternative splicing atlas in livestock animals. The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos ta ...

ResiDB is a user-friendly sequence similarity-dependent database manager for bacteria, fungi, viruses, protozoa, invertebrate, plants, archaea, environmental and whole genome shotgun sequence data. Create a new database Access existing databases Loa ...

an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific per ...

A dedicated database of non-B cell derived immunoglobulin variable region. Non-B cell derived ImmunoGlobulin Variable region Database. Welcome to NBIGV, a database dedicated to organizing and characterizing non-B cell derived immunoglobulins.

database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavio ...

The Spirochetes Genome Browser

Human disease-related phenotypes in model organisms

European mutant mice pathology database: histopathology photomicrographs and macroscopic images

The goal of the Genome Reviews project is to provide an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Genome Reviews are curated versions of EMBL/GenBank/DDBJ dat ...

Unambiguous insertions in the same subgenic regions of annotated mouse genes

The COGEME phytopathogen EST database currently contains expressed sequence tags (ESTs) from eleven species of phytopathogenic fungi and two oomycete species. In order to reduce sequence redundancy, sequence assembly software was used to join togethe ...

A database of quorum-sensing peptides

Full-length pig cDNA libraries and ESTs

The Spirochetes Genome Browser

Functional network of mouse genes

Nonhuman Primate Reference Transcriptome Resource

Sea urchin Strongylocentrotus purpuratus genome database

A database of Translation Initiation Sites

DataBase of Transcriptome in Mouse Early Embryos

Eukaryotic pseudogenes assigned to different protein families

Links from human disease to natural variation data in C. elegans

Database server for cleansed EST libraries

Phylogenetic patterns of genes from the Ensembl database

Genomic information on chicken and other avian species

Embryonic development of the mouse, chicken, zebrafish and human

A curated genome expression database of Oikopleura dioica

Searchable prototype experimental evolutionary database

ChIP-Seq and DNase-Seq data in human and mouse

CRISPR single guide RNAs to zebrafish genes

piggyBac transposon insertions in the mouse genome.

spatio-temporal gene expression patterns indipteran embryos

Orthologous and Paralogous Transcripts in Clades

The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, i ...

Heritability data for various species with trait-associated genomic loci

CASTLE (Computational Analysis of SynThetic LEthals) is a collection of synthetic lethal data for various pathogenic organisms, generated computationally. Here, you can find synthetic lethal genes and reactions for more than 70 organisms.

Gene indices of human, mouse, zebrafish, Arabidopsis, and Drosophila

The largest integrated microbial knowledge base.

Conserved syntenies for various animal, plant and bacterial genomes

Annotation and visualization of genome structure for Affymetrix exon array analysis

Plant transfer RNA database.

A dynamic, open and global database on crop pollination

MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.

A comprehensive mitochondrial genome database for Mollusca.

University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data

This is the Schizosaccharomyces japonicus genome database.

Information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies.

A phylogeny-based tool for comparative genomics

Mycobacterium leprae genome database.

A comprehensive database of long inverted repeats in eukaryotic genomes.

A web application gathering information about food enzyme preparations available on the European market.

A PROkaryotic Chromatin ImmunoPrecipitation DataBase

Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo scrip ...

Cre transgenic mouse lines with links to corresponding publications and to contact information for requests.

Knowledgebase of Microbes’ Battling Agents for Therapeutics.

An updated database for PTM dynamics in human, mouse, rat and yeast.

A comprehensive database for profiling prokaryotic pan-genome dynamics.

An integrative database of the expression dynamics of proteins in response to hypoxia in animals.

Semantic-based detection of redundancies to unify protein-protein interaction databases.

A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.

A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

dbCNS is a database for conserved noncoding sequences.

Database and analysis platform for gene expression and alternative splicing of fish species.

A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis.

A Database of Essential Genes Predicted Using Features From Interaction Networks.

DupScan is a database for visualizing and predicting vertebrate synteny and genome duplication.

The Chordata Olfactory Receptor Database (CORD) build from the annotation data from the command line tool Genome2OR

A collection of genes and proteins involved in human and yeast cell cycle.

A platform dedicated to the visualization and analysis of protist co-expression and co-function networks.

The SNPSTR database contains the SNP-STR/microsatellite compound markers in the five model species, where sufficient SNP information exists in both of the NCBI and Ensembl databases. These species are human (Homo sapiens), mouse (Mus musculus), rat ( ...

ExVe is the knowledge base of orthologous proteins identified in fungal extracellular vesicles.

PaxDb contains estimated abundance values for a large number of proteins in several different species. Furthermore, it contains information about inter-species variation of protein abundances.

MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex an ...

GAIA (G-quAdruplexes In Alive creature) is a user-friendly database with a web interface that can be used to query a data set containing pG4s in diverse species from all three living kingdoms.

Compilation, curation and exploration of a knowledgebase of environmental neurotoxicants specific to mammals. Neurotoxicants are an important class of hazardous chemicals.

ModelMatcher is a scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research.

An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle.

An integrated Web-database for bovine sequencing variations and selective signatures.

MycoWiki is organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae.

The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.

AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.

This website contains implementations of the MGT for various species. The MGT and metadata is searchable to allow identification of GTs associated with spatial, temporal or clinical characteristics.

FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles.

ZebraShare is intended to help establish fruitful collaborations by sharing mutant fish lines, and information about these mutants, particularly when authors do not otherwise see a clear path to publication.

The Postsynaptic Interaction Database is a comprehensive resource of the human postsynaptic (PS) binary protein-protein interactions. It contains experimental and computational evidence about interactions, along with structural and disease-related in ...

The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.

Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

The (Zebrafish) Xenograft Phenotype Interactive Repository (Xe.Ph.I.R) is an online database for describing how human cancer behaves when engrafted in zebrafish embryos. We provide representative images of the first days of cancer development post-en ...

Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

CRITTERBASE, a publicly accessible data warehouse and interactive portal that currently hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data for 18,644 samples and 3,664 benthic taxa (2,824 of which at ...

A web-based application for molecular identification of Prototheca species.

Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (htt ...

This database collects predicted drug targets in 150 pathogen species. The structural details of the drug mode of binding are also provided. Predictions are made using the information coming from drug-target three-dimensional complexes and by exploit ...

The Animal Proteome Database (AniProtDB) is a comprehensive collection of proteomes from 100 species spanning 21 animal phyla. In addition to providing open access to this collection of high-quality metazoan proteomes, information on predicted protei ...

Retrieving contents of BacDive and related information resources in a machine-readable form. BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers seve ...

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide ...

TEx-MST is a novel bioinformatic database for providing the valuable expression information of MANE-select transcripts in normal human tissues.

ChIP-Atlas is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.

A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computatio ...

database for eukaryotic single-exon coding sequences. Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to det ...

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations ...

Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

YPIBP is an inclusive database consisting of all the members of phosphatidylinositols-binding proteins which are collected from high-throughput proteome and lipid array studies, QuickGO and a rigorous literature mining. Cumulatively, across all PI, t ...

A comprehensive organelle genomes database for algae cpDNA and mtDNA. Algae is the earliest evolutionary biological group on the earth, are thought to have appeared at least 2.6 billion years ago. As the most complex biological group, algae have sho ...

A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite A ...

Metal binding sites, antigen epitopes, and drug binding sites are viral protein hotspots that control how viruses interact with their hosts. Like Google maps organizes and annotates points of interest on the planet, virus-M-E-D (Metal binding sites, ...

Tunicates are lower chordates that include among others the two ascidians Ciona intestinalis and Ciona savignyi. This subphylum is particularly interesting because it shares many developmental and physiological characteristics, as well as basic gene ...

ABA (Ascidian Body Atlas) is a digital 3D atlas of ascidian embryo development and gene expression pattern. Our 3D embryo images were reconstructed from more than 3,000 high-resolution real images acquired by a confocal laser microscopy in different ...

TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. ...

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and pr ...

Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not ye ...

The Mammalia Polymorphism Database (1) is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Mammalia class grouped by name of organism and gene. It allows the search for any polymorphic set accordi ...