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The 2019 Nucleic Acids Research Molecular Biology Database Collection

Table 1. Descriptions of new online databases in the 2019 NAR Database issue

Database  URL  Brief description 
AleDB  Mutations from Adaptive Laboratory Evolution experiments 
AlloMAPS  Allosteric signaling and mutations in proteins 
AmtDB  Ancient mitochondrial DNA 
Ancestral Genomes  Reconstructed ancestral genomes 
AWESOME  Impact of SNPs on post-translational modifications 
Bactome  Sequences, transcriptomes and phenotypes of clinical isolates of Pseudomonas auruginosa 
CAGm  Catalog of all germline microsatellites 
CancerSEA  Cancer single-cell state atlas 
CancerSplicingQTL  Splicing quantitative trait loci in cancer 
CellMarker  Cell markers in human and mouse 
Cell Model Passports  Human cancer cell models 
ChIPprimersDB  qPCR oligonucleotide primers for chromatin immunoprecipitation (ChIP) 
CMAUP  Collective molecular activities of useful plants 
CoevDB  Pairwise nucleotide coevolution 
CRISPRlnc  Validated CRISPR/Cas9 sgRNAs for model organism lncRNAs 
Cucurbit Genomics Database  Genomics of the Cucurbitaceae family 
dbAMP  Antimicrobial peptide sequences, structures and properties 
DSMNC  Database of somatic mutations in normal cells 
EDK  Editome disease knowledgebase 
EncoMPASS  Encyclopedia of membrane proteins analyzed by structure and symmetry. 
EndoDB  Gene expression in endothelial cells 
ENPD  Eukaryotic nucleic acid binding proteins 
ETCM  Encyclopedia of Traditional Chinese Medicine 
EVmiRNA  miRNA in extracellular vesicles 
EWAS Atlas  Epigenome-Wide Association Studies 
EWASdb  Epigenome-Wide Association Studies Atlas 
FusionGDB  Fusion Gene annotation DataBase 
gcMeta  Microbiome research data 
Genome Properties  Pathways and other properties represented by sets of protein families 
HACER  Human ACtive Enhancer to interpret Regulatory variants 
HmtVar  Human mitochondrial DNA variants 
iDOG  Dog data on genes, SNPs, diseases etc. 
iProX  Proteomics datasets 
jPOSTdb  Japan ProteOme STandard environment 
KinaMetrix  Protein kinase models, conformations and ligands 
liqDB  Small RNA expression profiles in biofluids 
LncBook  Human lncRNA knowledgebase 
MemProtMD  Membrane Proteins Embedded in Lipid Bilayers 
MethMotif  Transcription factor binding motifs coupled with DNA methylation profiles 
NucMap  Nucleosome positioning map across species 
OncoBase  Regulatory somatic mutations in human cancers 
OpenProt  Eukaryotic coding potential and proteomes 
Pancan-meQTL  Methylation quantitative trait loci in cancer 
PDX Finder  Patient-derived xenograft models 
PED  Plant Editosome Database 
PreMedKB  Precision medicine knowledgebase 
piRTarBase  piRNA targeting sites 
Plasmid Atlas  Plasmid annotations and metadata 
PLSDB  Plasmid annotations and metadata 
PopHumanScan  Positively selected regions of the human genome 
qPhos  Protein phosphorylation dynamics 
RetroRules  Reaction rules for synthetic biology 
RNact  Experimental and predicted protein–RNA interactions in human and mouse 
SAGD  Sex-associated gene database 
SEdb  Super-enhancer database 
SSRome  Microsatellites in all organisms 
SymMap  Traditional chinese medicine including symptom mapping 
Translocatome  Translocating human proteins 
Trips-Viz  Transcriptome browser 
UniLectin  Lectin structure and function 
ViBrism DB  Tomographic transcriptome and co-expression networks in mouse brain 
Victors  Virulence factors 
VMH  Virtual metabolic human 
YeastRGB  Expression and localization of yeast proteins 

Table 2. Updated descriptions of databases most recently published elsewhere

Database  URL  Brief description 
CADD  Combined annotation-dependent depletion 
GENCODE  Reference annotation for the human and mouse genomes. 
glycosciences.DB  Glyco-related databases 
Haemopedia  Haematopoietic expression data 
HumanNet  Human gene functional network 
LncACTdb  lncRNA–miRNA–gene interactions 
MoonDB  Known and predicted multifunctional proteins in model organisms 
OrthoInspector  Orthologous relations and phylogenetic profiling 
piRBase  piRNA function and annotation 
Stemformatics  Stem cell and other cell-specific gene expression 
UNITE  Internal transcribed spacer sequences for fungal identification 
Vesiclepedia  Extracellular vesicles 


Souce: Nucleic Acids Research    2019-03-09