Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
Islander - Database of Genomic Islands United States 4unstable1.16
The tmRNA website - The tmRNA website United States 300unstable13.20
UniProt - The Universal Protein Resource United Kingdom 13605unstable826.02
InterPro - Protein sequence analysis & classification United Kingdom 5033alive279.61
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
OMA - The Orthologous Matrix project United Kingdom 153unstable13.99
OrthoDB - Orthologs Database Switzerland 468unstable39.78
COG - Clusters of Orthologous Genes United States 11125unstable185.42
MBGD - Microbial Genome Database Japan 279alive18.23
MoonProt - Moonlighting Proteins Database United States 20alive6.47
REBASE - The Restriction Enzyme Database United States 927alive61.80
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.40
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable11.04
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable24.62
PAIDB - Pathogenicity Island Database Korea Rep. 110unstable7.62
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161unstable13.60
CollecTF - Database of Transcription Factor Binding Sites United States 31dead0.00
TCDB - Transporter Classification Database United States 87alive21.53
MEROPS - The peptidase Database United Kingdom 1760unstable67.89
Ensembl Genomes - Ensembl Genome Annotation System United Kingdom 293alive36.63
IMG - Integrated Microbial Genomes United States 568unstable17.04
DEG - Database of Essential Genes China 573alive40.93
PATRIC - Pathosystems Resource Integration Center United States 279unstable30.69
BacDive - Bacterial Diversity Metadatabase Germany 8alive2.00
MetaRef - A pan-genomic database for microbial genomics Italy 9unstable1.62
RDP - Ribosomal Database Project United States 11954alive433.89
SILVA - High quality ribosomal RNA databases Germany 3927unstable82.11
RhizoBase Japan 19unstable4.51
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive17.49
BacMet - Antibacterial Biocide and Metal Resistance Genes Database Sweden 16unstable3.80
RefSeq - Reference Sequence Database United States 6794unstable132.11
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable8.78
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive5.29
KEGG OC - KEGG Ortholog Cluster Japan 37alive7.40
OrtholugeDB - A Bacterial and Archaeal Orthology Resource Canada 17alive3.37
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive0.99
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive4.75
SecReT4 - Type IV Secretion System Resource China 21unstable3.95
SEVA - Standard European Vector Architecture Spain 87alive17.40
GEO - Gene Expression Omnibus United States 9384unstable205.27
StreptomeDB Germany 28unstable4.54
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.56
DBG2I - Database for bacterial group II introns Canada 37unstable2.47
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.27
ProGlycProt - Prokaryotic Glycoproteins India 13unstable1.89
GOLD - Genomes On Line Database United States 1646unstable26.06
BacMap Canada 47alive3.62
DBETH - Database of Bacterial ExoToxins India 20alive3.20
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable8.06
VFDB - Virulence Factor Database China 448alive34.46
UniPathway - UniPathway Switzerland 54unstable6.84
WikiPathways - WikiPathways Netherlands 228unstable17.10
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive4.62
RNAMDB - RNA Modification Database United States 1297unstable38.91
PSORTdb Canada 191unstable13.08
OMPdb - A database of ß-barrel outer membrane proteins from Gram-negative bacteria Greece 28alive3.96
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
CAMERA United States 257unstable30.11
ODB - Operon DataBase Japan 79unstable6.85
Effective - Effective Germany 48alive6.79
TADB - Toxin-antitoxin Data Base China 94unstable12.62
Protegen - Protective Antigens United States 28unstable3.52
RAC - Repository of Antibiotic Australia 15dead0.00
MEDIC - CTD's MEDIC disease vocabulary United States 54alive9.00
BactPepDB - Bacteria Peptide Database France 3alive0.74
FusoBase - online Fusobacterium comparative genomic analysis platform Malaysia 0unstable0.00
PolysacDB India 4alive0.67
WALTZ-DB - database of amyloid-forming peptides Belgium 0alive0.00
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.74
UniCarb-DB - UniCarb-DB Australia 65dead0.00
CORE United States 76unstable10.31
GCM - Global Catalogue of Microorganisms China 7alive1.40
TRACTOR_DB - TRAnscription FaCTORs' predicted binding sites in prokaryotic genomes Cuba 49unstable3.54
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.05
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive29.84
ACLAME - A CLAssification of Mobile genetic Elements Belgium 211alive14.77
ISbrowser - Insertion Sequences Browser France 18unstable0.43
Recode-2 Ireland 35alive4.29
CMR - Comprehensive Microbial Resource United States 577unstable28.17 - Integrated Database Resource for Marine Ecological Genomics Germany 42unstable3.99
MiST2 - Microbial Signal Transduction Database United States 147unstable11.94
MetaBioME - Comprehensive Metagenomic BioMining Engine Japan 36alive4.45
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
GeMInA - Genomic Metadata for Infectious Agents United States 15unstable1.37
ASAP - A Systematic Annotation Package for Community Analysis of Genomes United States 54dead0.00
SRPDB - Signal Recognition Particle Database United States 94unstable5.09
GtRNAdb - Genomic tRNA Database United States 378alive41.58
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable3.41
Voronoia - Voronoia Germany 52alive5.78
ATGC - Alignable Tight Genomic Clusters United States 38alive4.22
OperonDB - A Comprehensive Database of Predicted Operons in Microbial Genomes United States 69alive7.59
APD - Antimicrobial Peptide Database United States 572alive62.92
OligoArrayDb - Pangenomic Oligonucleotide Microarray Probe Sets Database United States 8unstable0.68
GISSD - Group I Intron Sequence and Structure Database China 54unstable3.29
ncRNAdb - Noncoding RNAs database Poland 53alive4.82
TransportDB - TransportDB United States 298alive27.09
TMBETA-GENOME Japan 20dead0.00
NMPDR - National Microbial Pathogen Data Resource United States 90unstable7.45
VNTRDB - Variable Number Tandem Repeat Database Taiwan 34dead0.00
OrthoMCL-DB - Querying a Comprehensive Multi-species Collection of Ortholog Groups United States 516unstable30.53
Pathguide - the Pathway Resource List United States 310alive25.57
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive22.43
dbSNP - Single Nucleotide Polymorphism Database United States 3381unstable62.28
COMBREX-DB - COMBREX database United States 0alive0.00
EK3D - E.coli Kantigen 3D structure Database India 0alive0.00
EffectiveDB - EffectiveDB Austria 0alive0.00
EBI - The European Bioinformatics Institute United Kingdom 610unstable16.27
HPMCD - Human Pan-Microbe Communities Database United Kingdom 1unstable0.47
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.49
BacWGSTdb - Bacterial Whole Genome Sequence Typing database China 1unstable0.47
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive2.25
Assembly United States 4unstable0.66
DESM - Microbial Knowledge Exploration Systems Saudi Arabia 1unstable0.44
sRNATarBase - sRNATarBase China 32unstable2.28
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.49
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive1.00
GSA - Genome Sequence Archive China 4alive3.84
antiSMASH-DB - antibiotics & Secondary Metabolite Analysis SHell database Denmark 2unstable0.76
ANItools China 6alive1.50
Abasy Atlas - Across-bacteria systems Atlas Mexico 1alive0.48
MAHMI - Mechanism of Action of the Human MIcrobiome Spain 0alive0.00
OCaPPI-Db - Oligonucleotide Capture Probes for Pathogen Identification Database France 0unstable0.00
SilkPathDB - Silkworm Pathogen Database China 0unstable0.00
Carotenoids Database - Carotenoids Database Japan 0alive0.00
WikiGenomes United States 0alive0.00
Pro54DB - σ54 promoter database China 0unstable0.00
ICG - A knowledgebase of Internal Control Genes for RT-qPCR normalization China 0alive0.00
* Citations derived from Google Scholar.