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 4alive2.00
The tmRNA website - The tmRNA website United States 300alive15.79
UniProt - The Universal Protein Resource United Kingdom 13605alive1036.07
InterPro - Protein sequence analysis & classification United Kingdom 5033alive296.06
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive60.39
OMA - The Orthologous Matrix project United Kingdom 153unstable22.95
OrthoDB - Orthologs Database Switzerland 468alive52.00
COG - Clusters of Orthologous Genes United States 11125unstable272.56
MBGD - Microbial Genome Database Japan 279alive19.73
MoonProt - Moonlighting Proteins Database United States 20alive10.00
REBASE - The Restriction Enzyme Database United States 927alive66.21
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable3.72
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable16.67
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable51.69
PAIDB - Pathogenicity Island Database Korea Rep. 110unstable7.88
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161alive20.13
CollecTF - Database of Transcription Factor Binding Sites United States 31dead0.00
TCDB - Transporter Classification Database United States 87alive29.00
MEROPS - The peptidase Database United Kingdom 1760unstable102.89
Ensembl Genomes - Ensembl Genome Annotation System United Kingdom 293alive41.86
IMG - Integrated Microbial Genomes United States 568unstable28.40
DEG - Database of Essential Genes China 573alive44.08
PATRIC - Pathosystems Resource Integration Center United States 279unstable26.97
BacDive - Bacterial Diversity Metadatabase Germany 8alive2.67
MetaRef - A pan-genomic database for microbial genomics Italy 9unstable2.85
RDP - Ribosomal Database Project United States 11954alive450.57
SILVA - High quality ribosomal RNA databases Germany 3927unstable129.59
RhizoBase Japan 19alive6.27
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive19.68
BacMet - Antibacterial Biocide and Metal Resistance Genes Database Sweden 16unstable5.01
RefSeq - Reference Sequence Database United States 6794unstable195.83
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable9.99
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive6.62
KEGG OC - KEGG Ortholog Cluster Japan 37alive9.25
OrtholugeDB - A Bacterial and Archaeal Orthology Resource Canada 17alive4.21
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive1.24
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive5.94
SecReT4 - Type IV Secretion System Resource China 21unstable4.83
SEVA - Standard European Vector Architecture Spain 87alive21.75
GEO - Gene Expression Omnibus United States 9384unstable306.54
StreptomeDB Germany 28alive6.79
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.98
DBG2I - Database for bacterial group II introns Canada 37unstable4.22
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.49
ProGlycProt - Prokaryotic Glycoproteins India 13alive2.52
GOLD - Genomes On Line Database United States 1646unstable40.40
BacMap Canada 47alive3.92
DBETH - Database of Bacterial ExoToxins India 20alive3.84
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable9.57
VFDB - Virulence Factor Database China 448alive37.33
UniPathway - UniPathway Switzerland 54unstable7.13
WikiPathways - WikiPathways Netherlands 228unstable28.73
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive5.39
RNAMDB - RNA Modification Database United States 1297unstable34.40
PSORTdb Canada 191unstable13.53
OMPdb - A database of ß-barrel outer membrane proteins from Gram-negative bacteria Greece 28alive4.62
VKCDB - voltage-gated potassium channels databse Canada 34alive2.62
CAMERA United States 257alive41.98
ODB - Operon DataBase Japan 79alive9.88
Effective - Effective Germany 48alive7.92
TADB - Toxin-antitoxin Data Base China 94unstable14.26
Protegen - Protective Antigens United States 28unstable4.11
RAC - Repository of Antibiotic Australia 15dead0.00
MEDIC - CTD's MEDIC disease vocabulary United States 54alive10.80
BactPepDB - Bacteria Peptide Database France 3alive0.98
FusoBase - online Fusobacterium comparative genomic analysis platform Malaysia 0unstable0.00
PolysacDB India 4alive0.80
WALTZ-DB - database of amyloid-forming peptides Belgium 0alive0.00
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.85
UniCarb-DB - UniCarb-DB Australia 65dead0.00
CORE United States 76unstable12.03
GCM - Global Catalogue of Microorganisms China 7alive1.75
TRACTOR_DB - TRAnscription FaCTORs' predicted binding sites in prokaryotic genomes Cuba 49unstable3.88
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.25
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive32.69
ACLAME - A CLAssification of Mobile genetic Elements Belgium 211alive15.91
ISbrowser - Insertion Sequences Browser France 18unstable0.69
Recode-2 Ireland 35alive4.95
CMR - Comprehensive Microbial Resource United States 577alive36.06 - Integrated Database Resource for Marine Ecological Genomics Germany 42unstable5.58
MiST2 - Microbial Signal Transduction Database United States 147unstable19.11
MetaBioME - Comprehensive Metagenomic BioMining Engine Japan 36alive5.09
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
GeMInA - Genomic Metadata for Infectious Agents United States 15alive2.12
ASAP - A Systematic Annotation Package for Community Analysis of Genomes United States 54dead0.00
SRPDB - Signal Recognition Particle Database United States 94unstable7.78
GtRNAdb - Genomic tRNA Database United States 378alive47.25
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable5.26
Voronoia - Voronoia Germany 52alive6.50
ATGC - Alignable Tight Genomic Clusters United States 38alive4.75
OperonDB - A Comprehensive Database of Predicted Operons in Microbial Genomes United States 69alive8.54
APD - Antimicrobial Peptide Database United States 572alive70.07
OligoArrayDb - Pangenomic Oligonucleotide Microarray Probe Sets Database United States 8unstable0.66
GISSD - Group I Intron Sequence and Structure Database China 54unstable4.20
ncRNAdb - Noncoding RNAs database Poland 53alive5.30
TransportDB - TransportDB United States 298alive29.80
TMBETA-GENOME Japan 20dead0.00
NMPDR - National Microbial Pathogen Data Resource United States 90unstable8.55
VNTRDB - Variable Number Tandem Repeat Database Taiwan 34dead0.00
OrthoMCL-DB - Querying a Comprehensive Multi-species Collection of Ortholog Groups United States 516unstable28.61
Pathguide - the Pathway Resource List United States 310alive27.90
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive26.17
dbSNP - Single Nucleotide Polymorphism Database United States 3381unstable92.04
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 610unstable23.87
HPMCD - Human Pan-Microbe Communities Database United Kingdom 1alive1.00
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.96
BacWGSTdb - Bacterial Whole Genome Sequence Typing database China 1unstable0.94
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive3.00
Assembly United States 4unstable1.88
DESM - Microbial Knowledge Exploration Systems Saudi Arabia 1unstable0.91
sRNATarBase - sRNATarBase China 32unstable3.70
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.97
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive2.00
GSA - Genome Sequence Archive China 4alive4.00
antiSMASH-DB - antibiotics & Secondary Metabolite Analysis SHell database Denmark 2unstable1.52
ANItools China 6alive2.00
Abasy Atlas - Across-bacteria systems Atlas Mexico 1alive1.00
MAHMI - Mechanism of Action of the Human MIcrobiome Spain 0unstable0.00
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.