Tag: model organisms


Found 204 sources
Source Match ReputationScore*

UCSC Genome Browser database


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.
100%

Human Protein Atlas


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 ...
89%

Kyoto Encyclopedia of Genes and Genomes


KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by geno ...
86%

Biological General Repository for Interaction Datasets


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.
80%

IUPHAR/BPS Guide to PHARMACOLOGY


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 ...
79%

Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource


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. Data includes gene characterization, nomenclature, mapping, gene homo ...
69%

The Human Metabolome Database


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.
68%

FlyBase


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 ...
66%

Saccharomyces Genome Database


The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
64%

Immune Epitope Database


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 ...
63%

WormBase


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 ...
61%

Eukaryotic Pathogen Database Resources


EuPathDB is an integrated database covering the eukaryotic pathogens. While each of the taxonomic groups within this resource is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to a ...
60%

Pseudomonas Genome DB


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.
60%

MEROPS


The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
60%

TRANSFAC


Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.
59%

NCBI Gene


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 ...
59%

The Zebrafish Information Network


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 ...
59%

Expression Atlas


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 ...
59%

JASPAR


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 ...
59%

The Arabidopsis Information Resource


The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
58%

Phytozome


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 ...
57%

PRotein Ontology


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 ...
55%

Xenopus laevis and tropicalis biology and genomics resource


Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the li ...
54%

Insertion Sequence Finder


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 ...
53%

Yeast GFP fusion localization database (yeastgfp)


Yeast GFP fusion localization database.
53%

Gene Ontology Annotation 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 ...
52%

PomBase


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 ...
52%

BRENDA tissue / enzyme source


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.
51%

TDR Targets


Identification and ranking of targets and bioactive compounds against neglected tropical diseases. TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and che ...
50%

EcoCyc E. coli Database


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 ...
49%

Virulence Factor Database


VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).
49%

Interologous Interaction Database


I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs).
49%

TriTrypDB


TriTrypDB 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 ...
48%

CRISPRFinder


Detects this family of direct repeats found in the DNA of many bacteria and archaea.
47%

Yeast Searching for Transcriptional Regulators and Consensus Tracking


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 ...
47%

PlasmoDB


PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.
47%

PLEXdb


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 ...
47%

Database of Bacterial Exotoxins for Human


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.
47%

NCBI Taxonomy Database


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.
47%

neXtProt


neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.
46%

Database of Orthologous Groups


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 ...
46%

Ribosomal Database Project (RDP-II)


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 ...
46%

e-Mouse Atlas


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 ...
46%

Candida Genome Database


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 ...
45%

MiST 3.0: Microbial Signal Transduction database


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 ...
45%

Ensembl Rat Genome Browser


The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).
45%

MitoMiner


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 ...
45%

IMGT/3Dstructure-DB


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 ...
44%

Protein Interaction Network Analysis platform


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 ...
44%

Online GEne Essentiality database


Online GEne Essentiality database
44%

Collection of Anti Microbial Petides R3


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 ...
44%

PhylomeDB


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.
44%

Toxoplasma Genomics Resource


ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.
44%

BIND: The Biomolecular Interaction Network Db


Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
44%

dictyBase


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 ...
44%

Legume Information System


The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.
43%

GeneDB


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 ...
43%

Codon Usage Database


Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
43%

A CLAssification of Mobile genetic Elements


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.
43%

GeneWeaver


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 ...
43%

GiardiaDB


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.
42%

AgBase


AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
42%

MicrobesOnline


A suite of Web-based tools for comparative genomics
42%

Yeast gene order browser


Tool for visualising the syntenic context of any gene from several yeast genomes.
42%

BeetleBase


BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.
42%

Cryptosporidum Genomics Resource


CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community resear ...
41%

FlyCircuit


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 ...
41%

NCBI BioProject


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 ...
41%

Hymenoptera Genome Database


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 ...
41%

Escherichia coli strain K12 genome database


The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.
41%

cis-Regulatory Element 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.
41%

TrichDB


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 ...
40%

Mammalian Protein Localization Database


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.
40%

Integrative and Conjugative Elements in Bacteria


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 ...
40%

The DNA Replication Origin Database


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 ...
40%

SOURCE


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 ...
40%

Plant Resistance Gene Database


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.
40%

Banana Genome Hub


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.
39%

VBASE2


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.
39%

Comprehensive Yeast Genome Database


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 ...
39%

Assembling the Fungal Tree of Life


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.
39%

DOE Joint Genome Institute Genome Portal


The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.
39%

JGI Genome Portal


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 ...
39%

National Microbial Pathogen Data Resource


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 ...
39%

Mouse Proteome Project


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 ...
39%

TubercuList


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 ...
39%

Newt-omics


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 ...
39%

MiCroKiTS


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 ...
39%

SAGEmap


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 ...
39%

The Improved Database Of Chimeric Transcripts and RNA-Seq Data


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 ...
39%

NextBio gene-centric data


The platform enables biologists to examine a gene, protein, compound or disease of interest in a global, biological, or clinical context.
39%

RiceXPro


Rice transcriptome under natural conditions
38%

Dragon Antimicrobial Peptide Database


Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.
38%

PeroxisomeDB


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.
37%

Saccharomyces cerevisiae Transcription Factor Database


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 ...
37%

deepBase


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 ...
37%

Patrocles


Polymorphic miRNA-mediated gene regulation in vertebrates
37%

GenoList Genome Browser


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 ...
37%

Chlamydiae Database


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 ...
37%

PhylomeDB v3.0


It is a public database for genome-wide collections of gene phylogenies (phylomes). It is also a major source for phylogeny-based orthology and paralogy predictions. For each protein-coding gene in a seed genome, the database provides original and pr ...
36%

ParameciumDB


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 ...
36%

PreOpDB


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 ...
36%

BioMart Central


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 ...
36%

WorfDB - Worm ORF Database


Predicted proteins from C. elegans
36%

University of Minnesota Biocatalysis/Biodegradation Database


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 ...
36%

Genome Biology Ontology Language


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 ...
36%

PREX


PeroxiRedoxin classification indEX
36%

EchoBase


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.
36%

Eukaryotic Genes


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, ...
35%

PolyASite


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 ...
35%

CycleBase


Gene expression profiles from cell-cycle microarray studies
35%

MBGD - Microbial Genome Database


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 ...
35%

CyanoBase


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 ...
35%

HOMOLENS


Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.
35%

Legionella pneumophila genome database


Legionella pneumophila genome database.
35%

PAIR


Predicted Arabidopsis Interactome Resource
35%

Alliance of Genome Resources


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 ...
35%

P2CS


Prokaryotic 2-Component Systems database
35%

Protegen


Protective antigen database and analysis system
35%

Prokaryotic Glycoproteins Database


ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized eubacterial and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort ...
35%

REPAIRtoire


DNA repair pathways of human, yeast and E.coli
35%

Arabidopsis Hormone Database


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 ...
35%

DBASS5/3


Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites
34%

YPA


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 ...
34%

ROdent Unidentified Gene-Encoded large proteins


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 ...
34%

PolygenicPathways


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 ...
34%

Ciona intestinalis Protein Database


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 ...
34%

CUBE-DB


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 ...
34%

Isobase


IsoRank PPI Network Alignment Based Ortholog Database
34%

Nematodes.org


Wiki for coordinating nematode sequencing projects
34%

IEDB-3D


Structural data within the Immune Epitope Database
34%

AntigenDB


Sequence, structure, and other data on pathogen antigens
34%

Human Integrated Pathway Database


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 ...
34%

ODB - Operon database


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 ...
34%

MetaBase


Wiki database of biological databases
33%

GWIDD


Genome-WIde Docking Database: 3D structures of protein complexes
33%

SALAD


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 ...
33%

dbSNP-Q


GWAS prioritization tool
33%

gutMDisorder


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 ...
33%

Yeast KID


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.
33%

FusariumDB


Comparative genomics of Fusarium strains
33%

DNAtraffic


A database for systems biology of DNA dynamics during the cell life.
33%

RNA helicase database


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 ...
33%

diArk


A database of eukaryotic sequencing projects
33%

GELBANK


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 ...
33%

CADRE Genomes Browser


Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available.
32%

VKCDB - Voltage-gated K+ Channel Database


Voltage-gated potassium channel database
32%

MFunGD


MIPS mouse functional genomics database
32%

KUPS


Interacting and non-interacting protein pairs
32%

The database of eukaryotic RNA binding proteins


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 ...
32%

PartiGeneDB


Assembled partial genomes for ~250 eukaryotic organisms
32%

ePlant


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.
32%

Pathema


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 ...
31%

PhEVER


Phylogenetic Exploration of Viruses and their Evolutionary Relationships
31%

The catfish genome database (cBARBEL)


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 ...
31%

snoDB


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
31%

PhenoModifier


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 ...
31%

Microbial advanced database organisation (Micado)


Microbial genome and functional analysis of Bacillus subtilis.
31%

OHNOLOGS v2


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 ...
30%

AcrDB


anti-CRISPR operons
30%

3DIV


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 ...
30%

GPSDB


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.
30%

PlantAPAdb


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 ...
30%

DrLLPS


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 ...
30%

ePath


An online database towards comprehensive essential gene annotation for prokaryotes.
29%

PADS Arsenal


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.
29%

BacFITBase


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 ...
29%

Xanthusbase


Model organism database for the bacterium Myxococcus xanthus.
28%

PerMemDB


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 ...
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MSDB


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 ...
28%

TOFF


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 ...
28%

BiomeNet


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 ...
28%

Genomicus


The Spirochetes Genome Browser
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gcType


WDCM 10K sequencing projects
28%

Genome Reviews


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 ...
28%

MitoGenesisDB


Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis
28%

COGEME Phytopathogenic Fungi and Oomycete EST Database


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 ...
28%

bAciDB


AciDB is a database of about 600 manually curated acidophilic organisms, their genomic information and associated metadata.
26%

Birdbase


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 ...
26%

StrainInfo


The largest integrated microbial knowledge base.
26%

CEBA geoportail


A portal for geographic reference data for the Amazon.
26%

crystals MoS2


The site-symmetry induced representations of layer groups on the Bilbao Crystallographic Server.
26%

Mycobacterium leprae genome database


Mycobacterium leprae genome database.
26%

GenomeHubs


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 ...
26%

GenOrigin


A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.
26%

Cell cycle database (CellCycleDB)


A collection of genes and proteins involved in human and yeast cell cycle.
26%

PaxDb


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.
26%

Database of genes from NCBI RefSeq genomes


Database of genes from NCBI RefSeq genomes.
26%

Bovine Genome Variation Database (BGVD)


An integrated Web-database for bovine sequencing variations and selective signatures.
26%

Sugarcane Genome Hub


The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.
26%

GCGVD


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.
26%

Cocoa Genome Hub


The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.
26%

Genomicus-fungi


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.
26%

Genomicus-protists


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.
26%

Genomicus-metazoa


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.
26%

Genomicus-tunicates


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 ...
26%

TiPs


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 ...
26%

AniProtDB


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 ...
26%

BacDive WS


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 ...
26%

South Green Genome Hubs


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 ...
26%

ASlive


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 ...
26%

UPObase


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 ...
26%

Genomicus-plants


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.
26%

ClinEpiDB


An open-access clinical epidemiology database resource encouraging online exploration of complex studies. The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerat ...
26%

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