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 4unstable1.24
UniProt - The Universal Protein Resource United Kingdom 13605unstable884.33
InterPro - Protein sequence analysis & classification United Kingdom 5033alive279.61
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
OMA - The Orthologous Matrix project United Kingdom 153unstable14.86
COG - Clusters of Orthologous Genes United States 11125unstable196.01
MBGD - Microbial Genome Database Japan 279alive18.23
REBASE - The Restriction Enzyme Database United States 927alive61.80
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.45
rrnDB - Ribosomal RNA Operons Database United States 988unstable12.20
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable26.02
PAIDB - Pathogenicity Island Database Korea Rep. 110unstable7.62
Ensembl - Ensembl United Kingdom 12662alive783.46
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161unstable14.31
TCDB - Transporter Classification Database United States 87alive21.53
DEG - Database of Essential Genes China 573alive40.93
BacDive - Bacterial Diversity Metadatabase Germany 8alive2.00
MetaRef - A pan-genomic database for microbial genomics Italy 9unstable1.73
RDP - Ribosomal Database Project United States 11954alive433.89
SILVA - High quality ribosomal RNA databases Germany 3927unstable89.25
RefSeq - Reference Sequence Database United States 6794unstable139.65
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable9.18
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
GEO - Gene Expression Omnibus United States 9384unstable217.01
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.59
ProGlycProt - Prokaryotic Glycoproteins India 13unstable1.89
GOLD - Genomes On Line Database United States 1646unstable27.43
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable8.06
UniPathway - UniPathway Switzerland 54unstable6.75
RNAMDB - RNA Modification Database United States 1297unstable37.83
PSORTdb Canada 191unstable13.08
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
TADB - Toxin-antitoxin Data Base China 94unstable12.49
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.74
UniCarb-DB - UniCarb-DB Australia 65dead0.00
GCM - Global Catalogue of Microorganisms China 7alive1.40
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.05
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive30.46
ISbrowser - Insertion Sequences Browser France 18unstable0.47
Recode-2 Ireland 35alive4.29
CMR - Comprehensive Microbial Resource United States 577unstable29.87
Megx.net - Integrated Database Resource for Marine Ecological Genomics Germany 42unstable4.25
MiST2 - Microbial Signal Transduction Database United States 147unstable12.68
GtRNAdb - Genomic tRNA Database United States 378alive41.58
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable3.63
Voronoia - Voronoia Germany 52alive5.78
ATGC - Alignable Tight Genomic Clusters United States 38alive4.22
APD - Antimicrobial Peptide Database United States 572alive62.92
OligoArrayDb - Pangenomic Oligonucleotide Microarray Probe Sets Database United States 8unstable0.66
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 90alive7.85
VNTRDB - Variable Number Tandem Repeat Database Taiwan 34dead0.00
OrthoMCL-DB - Querying a Comprehensive Multi-species Collection of Ortholog Groups United States 516unstable29.67
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive22.43
COMBREX-DB - COMBREX database United States 0alive0.00
EBI - The European Bioinformatics Institute United Kingdom 610unstable17.28
HPMCD - Human Pan-Microbe Communities Database United Kingdom 1alive0.50
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.49
Assembly United States 4unstable0.70
NCBI - National Center for Biotechnology Information United States 16174unstable323.48
DESM - Microbial Knowledge Exploration Systems Saudi Arabia 1unstable0.46
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive4.50
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.49
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive1.00
ENA - European Nucleotide Archive United Kingdom 2398unstable76.51
GSA - Genome Sequence Archive China 4unstable3.80
GWAS Catalog United Kingdom 3886alive431.78
Carotenoids Database - Carotenoids Database Japan 0alive0.00
* Citations derived from Google Scholar.
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