Compilation Paper

Alphabetical List

Category/Paper List

Search Summary Papers

NAR Database Summary Paper

Nucleotide Sequence Databases

Cistrome Data Browser

Expression Atlas

Expression Atlas

miRNATissueAtlas

Ribocentre-switch

UTexas Aptamer Database

International Nucleotide Sequence Database Collaboration

EBI patent sequences

European Genome-phenome Archive (EGA)

European Nucleotide Archive

NCBI BioSample/BioProject

The Sequence Read Archive (SRA)

Coding and non-coding DNA

ACLAME - A Classification of Mobile genetic Elements

Ciliate IES-MDS database

CORG - A database for COmparative Regulatory Genomics

NPRD - Nucleosome Positioning Region Database

OriDB - The DNA Replication Origin Database

Plant repeat database

RefSeq (microbial)

Synthetic Gene Database

TIGR Plant Transcript Assembly database

UCbase and miRfunc

VISTA Enhancer Browser

Gene structure, introns and exons, splice sites

EDAS - EST-Derived Alternative Splicing Database

Spliceosome Database

Yeast Intron Database

Transcriptional regulator sites and transcription factors

AGRIS - Arabidopsis Gene Regulatory Information Server

CTCF Binding Site Database

DoOP - Databases of Orthologous Promoters

FlyFactorSurvey

ODB - Operon database

Plant Stress-Responsive Gene Catalog

SCPD - Saccharomyces cerevisiae promoter database

SKY/M-FISH and CGH

SpatialDB: a database for spatially resolved transcriptomes

Telomerase database

TRED - Transcriptional Regulatory Element Database

VISTA Enhancer Browser

RNA sequence databases

16S and 23S Ribosomal RNA Mutation Database

3D rRNA modification maps

5S Ribosomal RNA Database

AlphaFold Protein Structure Database

Cereal Small RNA Database

CORG - A database for COmparative Regulatory Genomics

Database for Bacterial Group II Introns

European rRNA database

G protein research platform

GtRDB - Genomic tRNA Database

HMDD v2.0 - Human microRNA Disease Database version 2.0

Human Proteoform Atlas

NCIR - Non-Canonical Interactions in RNA

ncRNAs database

Plant snoRNA DB

PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3Ã¢â‚¬Â² end sequencing

Ribosomal Database Project (RDP-II)

RNA Modification Database

T-psi-C: user friendly database of tRNA sequences and structures

The Small Subunit rRNA Modification Database

Yeast snoRNA Database

Coding and non-coding DNA

Protein sequence databases

A3D Model Organism Database

ConsensusPathDB

MultifacetedProtDB

General sequence databases

NCBI Protein database

PIR - Protein Information Resource

Protein properties

Minimotif miner

PFD - Protein Folding Database

Proteome-pI 2.0

Protein localization and _targeting

eSLDB - eukaryotic Subcellular Localization database

NMPdb - Nuclear matrix associated proteins database

NOPdb: Nucleolar Proteome Database

NPD - Nuclear Protein Database

OGRe - Organellar Genome Retrieval

Secreted Protein Database

THGS - Transmembrane Helices in Genome Sequences

Protein sequence motifs and active sites

ASC - Active Sequence Collection

COMe - Co-Ordination of Metals etc.

eF-site - Electrostatic surface of Functional site

ELM - Eukaryotic Linear Motif: functional sites in eukaryotic proteins

HRaP - Database of occurrence of HomoRepeats and Patterns in proteomes

Minimotif Miner

PhosphoSItePlus

Protein domain databases; protein classification

3DSwap: Database of Proteins involved in 3D domain Swapping

ADDA - A Domain Database

DomIns - Database of Domain Insertions

EVEREST - EVolutionary Ensembles of REcurrent SegmenTs

Protein Clusters

Databases of individual protein families

Animal Toxin Database

CSDBase - Cold Shock Domain database

Death Domain database

Defensins Knowledgebase

Degradome Database

GPCR NaVa database

gpDB - G-protein database

Heme Protein Database

HIV RT and Protease Sequence Database

Knottin database

Laminin Database

Lipase Engineering Database

OKCAM - now available at RhesusBase

Olfactory Receptor Database

PlantsP/PlantsT

Protein kinase resource

Ribonuclease P Database

RPG - Ribosomal Protein Gene database

Telomerase database

UCSD-Nature Signaling Gateway Molecule Pages

VKCDB - Voltage-gated K⁺ Channel Database

Structure Databases

Ensembl COVID-19 resource

NMDC Data Portal

T-cell COVID-19 Atlas

Transcriptional regulator sites and transcription factors

Small molecules

ChEBI - Chemical Entities of Biological Interest

Crystallography Open Database

CSD - Cambridge Structural Database

EDULISS (currently unavailable)

Bacterial CSDB (BCSDB)

Carbohydrate Structure Database (CSDB)

CCSD - Complex Carbohydrate Structure Database (CarbBank)

CSS - Carbohydrate Structure Suite

Glycan Fragment DB

Glycoconjugate Data Bank

Nucleic acid structure

NCIR - Non-Canonical Interactions in RNA

SARS-CoV RNA SSS

Protein structure

3DID - 3D interacting domains

CADB - Conformational Angles DataBase of Proteins

DisProt - Database of Protein Disorder

DomIns - Database of Domain Insertions

DSMM - a Database of Simulated Molecular Motions

eF-site - Electrostatic surface of Functional site

Genomic Threading Database

GTOP - Genomes To Protein structures

HOMSTRAD - Homologous Structure Alignment Database

IMGT/3Dstructure-DB

Jenalib: Jena Library of Biological Macromolecules

MolMovDB - Database of Macromolecular Movements

NPIDB (Nucleic acids ÃƒÂ¢Ã¢â€šÂ¬Ã¢â‚¬Å“ Protein Interaction DataBase)

PFD - Protein Folding Database

PMDB - Protein Model Database

Protein Geometry Database

RCSB Protein Data Bank

SCOP2 - Structural Classification Of Proteins

SMoS.2: Update of database of Structural Motifs in Superfamilies

SSToSS - Sequence-Structural Templates of Single-member Superfamilies

STAP refinement of NMRdb

Structure Superposition Database

SWISS-MODEL Repository

Genomics Databases (non-vertebrate)

Animal QTLdb and CorrDB

EWAS Open Platform

Gene Expression Nebulas

Regeneration Roadmap

Genome annotation terms, ontologies and nomenclature

Human Phenotype Ontology

IUBMB Nomenclature database

IUPAC Nomenclature database

MIRIAM Registry

Plant Ontology database

Protein Naming Utility

Taxonomy and identification

EBI Metagenomics

Ribosomal Database Project (RDP-II)

RIDOM - Ribosomal Differentiation of Medical Microorganisms

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data

General genomics databases

Animal Genome Size Database

Genome Project Database

Genomes OnLine Database (GOLD)

GtRDB - Genomic tRNA Database

Integr8 (formerly Proteome Analysis Database)

MBGD - Microbial Genome Database

Viral genome databases

HERVd - Human Endogenous Retrovirus database

HIV Drug Resistance Database

HIV RT and Protease Sequence Database

Influenza Research Database

IVDB - Influenza Virus Database

NCBI Viral genomes

Papillomavirus Episteme

SARS-CoV RNA SSS

Viral Bioinformatics Resource

ViralORFeome (discontinued)

Prokaryotic genome databases

ASAP - A Systematic Annotation Package

BSORF - Bacillus subtilis Open Reading Frames

CCDB - The CyberCell Database

Comparative Genometrics

DEG - Database of Essential Genes

Essential genes in E. coli

HGT-DB, Horizontal Gene Transfer-DataBase

meta.MicrobesOnline

ODB - Operon database

PAIDB - Pathogenicity Island Database

PATRIC, the bacterial bioinformatics database and analysis resource

PEC - Profiling of E. coli Chromosome

Pseudomonas Genome Database

UCSC Archaeal Genome Browser

VFDB - Virulence Factors Database

Unicellular eukaryotes genome databases

ApiDB - Apicomplexan DataBase

Aspergillus Genomes

CryptoDB - Cryptosporidium database

Diatom EST Database

MicrosporidiaDB

TGD - Tetrahymena Genome Database

ToxoDB - The Toxoplasma gondii Genome Database

Fungal genome databases

Magnaporthe grisea Database

AGD - Ashbya Genome Database

CADRE - Central Aspergillus Data Repository

CGD - Candida Genome Database

COGEME Phytopathogenic Fungi and Oomycete EST Database

EBI Metagenomics

Fungal Genome Size Database

OriDB - The DNA Replication Origin Database

SCMD - Saccharomyces cerevisiae Morphological Database

SCPD - Saccharomyces cerevisiae promoter database

SGD - Saccharomyces Genome Database

YDPM - Yeast Deletion Project

Yeast Intron Database

Yeast Resource Center

Yeast snoRNA Database

yMGV - Yeast microarray global viewer

Invertebrate genome databases

Digital Development Database

Drosophila polymorphism database

Hymenoptera Genome

i5k Workspace@NAL

InterActive Fly

KinG: Kinases in Genomes

Pristionchus.org

WDDD - Worm Developmental Dynamics Database

WorfDB - Worm ORF Database

Model organisms, comparative genomics

Mouse Genome Database

Metabolic and Signaling Pathways

antiSMASH database

Human Disease Ontology

IMGT® databases

IUPHAR/BPS Guide to Pharmacology

NCATS Inxight: Drugs

SwissBioisostere

Enzymes and enzyme nomenclature

Allosteric Database

CSA - Catalytic Site Atlas

EBI Enzyme Portal

Enzyme Nomenclature

Metabolic pathways

BioCarta Pathways

HMDB - The Human Metabolome Database

Metabolomics Workbench

MNXref/MetaNetX

MultitaskProtDB-II

Pathway Commons

WholeCellKB - Model Organism Databases for Comprehensive Whole-Cell Models

Protein-protein interactions

BioCarta Pathways

ConsensusPathDB

DroID - Drosophila Interactions Database

Dynamic Proteomics

HPID - Human Protein Interaction database

I2D - Interologous Interaction Database

IntAct Molecular Interaction Database

Inter-Chain Beta-Sheets

NCBI BioSystems

PathoPlantÃ‚Â®

PIG - Pathogen Interaction Gateway

Predictive Networks

Protein kinase resource

Protein-protein interfaces

STCDB - Signal Transduction Classification Database

The Cell Cycle DB

Signalling pathways

UCSD-Nature Signaling Gateway Molecule Pages

Human and other Vertebrate Genomes

Invertebrate genome databases

Model organisms, comparative genomics

ABA - Ascidian Body Atlas

Animal Genome Size Database

CORG - A database for COmparative Regulatory Genomics

Cre Transgenic Database

Ensembl Genomes

International Mouse Phenotyping Consortium Database

Monarch Initiative

Mouse Phenome Database

Mouse Phenome Database

MUGEN Mouse Database

OMIA - Online Mendelian Inheritance in Animals

PEDE - Pig Expression Data Explorer

TAED - The Adaptive Evolution Database

Human genome databases, maps and viewers

ENCODE Project at UCSC

Locus Reference Genomic sequences

The Chromosome 7 Annotation Project

TIARA - Total Integrated Archive of short-Read and Array

UCSC Genome Browser

UCSC Genome Browser

ENCODE Project at UCSC

H-Invitational Database, an integrated database of human genes and transcripts

HPRD - Human Protein Reference Database

Human Proteinpedia

IPI - International Protein Index

Mammalian Gene Collection

trome, trEST and trGEN

Human Genes and Diseases

ClinicalOmicsDB

Disease Ontology

Disease Ontology Knowledgebase

FusionNeoAntigen

The IUPHAR/BPS Guide to PHARMACOLOGY

General human genetics databases

CSVS - The Collaborative Spanish Variability Server

Exome Aggregation Consortium

Genetics Home Reference

HAGR - Human Ageing Genomic Resources

HCAD - Human Chromosome Aberration Database

HERVd - Human Endogenous Retrovirus database

IUPHAR/BPS Guide to Pharmacology

MSY Breakpoint Mapper

NIH Genetic Testing Registry

General polymorphism databases

1000 Genomes Selection Browser

Allele Frequency Net

Cypriot national mutation database

Database of Genomic Variants (DGV)

Database of Genomic Variants archive (DGVa)

GWAS Diagram Browser

Lynx: a database and knowledge extraction engine for integrative medicine

TPMD - Taiwan polymorphic microsatellite marker database

Cancer gene databases

Cancer RNA-Seq Nexus

Candidate Cancer Gene Database

CellLineNavigator

Colorectal Cancer Atlas

IARC TP53 Database

MutationAligner

Network of Cancer Genes

Pancreas Expression

Stem Cell Discovery Engine

Tumor Associated Gene database

UCSC Cancer Genomics Browser

UMD-BRCA1/BRCA2 databases

Gene-, system- or disease-specific databases

Autophagy Database

BCNTB bioinformatics

Digital Ageing Atlas

DNAreplication.net

ERGDB - Estrogen Responsive Genes Database

GOLD.db - Genomics Of Lipid-associated Disorders

HORDE - Human Olfactory Receptor Data Exploratorium

HPMR - Human Plasma Membrane Receptome

Imprinted Gene Catalogue

Lowe Syndrome Mutation Database

Organ System Heterogeneity DB

The Autism Chromosome Rearrangement Database

The Lafora Database

Microarray Data and other Gene Expression Databases

ABA - Ascidian Body Atlas

Allen Brain Atlas

CATMA - Complete Arabidopsis Transcriptome MicroArray

COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia

Expression Atlas

Expression Atlas

Gene Expression Barcode

GEO - Gene Expression Omnibus

GPX-Macrophage Expression Atlas

HPMR - Human Plasma Membrane Receptome

International Gene Trap Consortium Database

MAMEP - Molecular Anatomy of the Mouse Embryo Project

MEPD: A Medaka gene expression pattern database

NASCarrays (obsolete)

SpermatogenesisOnline

Stanford Tissue Microarray Database

yMGV - Yeast microarray global viewer

Proteomics Resources

Open Proteomics Database

Plasma Proteome Database

ProteomeXchange

Other Molecular Biology Databases

Cell Image Library

DNASU Plasmid Repository

Europe PubMed Central

ReplicationDomain (alias ChromosomeDomain)

StrainInfo.net Bioportal

The Cell Cycle DB

University of Pittsburgh Bioinformatics Resources Collection

Drugs and drug design

APD - Antimicrobial Peptide Database

BioMuta and BioExpress

CTD - Comparative Toxicogenomics Database

DART - Drug Adverse Reaction _targets

Defensins Knowledgebase

Exposome-Explorer

Herb Ingredient _targets

HIV Drug Resistance Database

IUPHAR/BPS Guide to Pharmacology

SwissBioisostere

TTD - Therapeutic _target Database

Molecular probes and primers

Addgene Repository Database

Human OligoGenome Resource

MPDB - Molecular Probe Database

Organelle databases

Chloroplast Genome Database

Organelle genomes

Plant Organelles Database

Mitochondrial genes and proteins

HmtDB - Human Mitochondrial DataBase

MitoBreak - The mitochondrial DNA breakpoints database

MPIM - Mitochondrial Protein Import Machinery

OGRe - Organellar Genome Retrieval

YDPM - Yeast Deletion Project

Plant databases

Chloroplast Genome Database

General plant databases

Cereal Small RNA Database

CR-EST - Crop ESTs

GÉnoPlante-Info

Leaf Senescence Database

MPIM - Mitochondrial Protein Import Machinery

PathoPlantÃ‚Â®

Plant DNA C-values database

Plant Ontology database

Plant repeat database

Plant snoRNA DB

Plant Stress-Responsive Gene Catalog

PlantsP/PlantsT

Plastid-LCGbase

PPDB: Plant Proteomics Database

TAED - The Adaptive Evolution Database

TIGR Plant Transcript Assembly database

Arabidopsis thaliana

AGRIS - Arabidopsis Gene Regulatory Information Server

Arabidopsis Hormone Database

Arabidopsis Mitochondrial Protein Database

Arabidopsis MPSS

Arabidopsis Nucleolar Protein Database

ASRP - Arabidopsis Small RNA Project

CATMA - Complete Arabidopsis Transcriptome MicroArray

GABI-Kat SimpleSearch database

NASCarrays (obsolete)

Plant Metabolomics

RARGE - RIKEN Arabidopsis Genome Encyclopedia

Oryza Tag Line

BGI-RISe - Beijing Genomics Institute Rice Information System

Manually Curated Database of Rice Proteins

Rice Annotation Database

Rice Gene Thresher

Rice Mutant Database

Rice Proteome Database

Medicago trunculata Database

Brassica Genome

Coffee Genome Hub

Diatom EST Database

Genome Database for Rosaceae

PoMaMo - Potato Maps and More

Shanghai Rapeseed Database

SoyKB - Soybean Knowledge Base

TED - Tomato Functional Genomics Database

TIGR Maize database

Immunological databases

GPX-Macrophage Expression Atlas

IPD - Immuno Polymorphism Database

IPD-HPA - Human Platelet Antigens

IPD-KIR - Killer-cell Immunoglobulin-like Receptors

MUGEN Mouse Database

Compilation Paper

Alphabetical List

Category/Paper List

Search Summary Papers

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