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
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
COG - Clusters of Orthologous Genes United States 11125unstable272.56
MBGD - Microbial Genome Database Japan 279alive19.73
REBASE - The Restriction Enzyme Database United States 927alive66.21
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable3.72
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
Ensembl - Ensembl United Kingdom 12662alive827.25
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161alive20.13
TCDB - Transporter Classification Database United States 87alive29.00
DEG - Database of Essential Genes China 573alive44.08
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
RefSeq - Reference Sequence Database United States 6794unstable195.83
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable9.99
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
GEO - Gene Expression Omnibus United States 9384unstable306.54
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.98
ProGlycProt - Prokaryotic Glycoproteins India 13alive2.52
GOLD - Genomes On Line Database United States 1646unstable40.40
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable9.57
UniPathway - UniPathway Switzerland 54unstable7.13
RNAMDB - RNA Modification Database United States 1297unstable34.40
PSORTdb Canada 191unstable13.53
VKCDB - voltage-gated potassium channels databse Canada 34alive2.62
TADB - Toxin-antitoxin Data Base China 94unstable14.26
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.85
UniCarb-DB - UniCarb-DB Australia 65dead0.00
GCM - Global Catalogue of Microorganisms China 7alive1.75
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.25
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive32.69
ISbrowser - Insertion Sequences Browser France 18unstable0.69
Recode-2 Ireland 35alive4.95
CMR - Comprehensive Microbial Resource United States 577alive36.06
Megx.net - Integrated Database Resource for Marine Ecological Genomics Germany 42unstable5.58
MiST2 - Microbial Signal Transduction Database United States 147unstable19.11
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
APD - Antimicrobial Peptide Database United States 572alive70.07
OligoArrayDb - Pangenomic Oligonucleotide Microarray Probe Sets Database United States 8unstable0.66
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
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive26.17
COMBREX-DB - COMBREX database United States 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
Assembly United States 4unstable1.88
NCBI - National Center for Biotechnology Information United States 16174unstable447.16
DESM - Microbial Knowledge Exploration Systems Saudi Arabia 1unstable0.91
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive9.00
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.97
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive2.00
ENA - European Nucleotide Archive United Kingdom 2398unstable107.91
GSA - Genome Sequence Archive China 4alive4.00
GWAS Catalog United Kingdom 3886alive485.75
Carotenoids Database - Carotenoids Database Japan 0alive0.00
* Citations derived from Google Scholar.
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