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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  http://aledb.org  Mutations from Adaptive Laboratory Evolution experiments 
AlloMAPS  http://allomaps.bii.a-star.edu.sg  Allosteric signaling and mutations in proteins 
AmtDB  https://amtdb.org  Ancient mitochondrial DNA 
Ancestral Genomes  http://ancestralgenomes.org  Reconstructed ancestral genomes 
AWESOME  http://www.awesome-hust.com  Impact of SNPs on post-translational modifications 
Bactome  https://bactome.helmholtz-hzi.de  Sequences, transcriptomes and phenotypes of clinical isolates of Pseudomonas auruginosa 
CAGm  http://www.cagmdb.org  Catalog of all germline microsatellites 
CancerSEA  http://biocc.hrbmu.edu.cn/CancerSEA  Cancer single-cell state atlas 
CancerSplicingQTL  http://www.cancersplicingqtl-hust.com  Splicing quantitative trait loci in cancer 
CellMarker  http://biocc.hrbmu.edu.cn/CellMarker  Cell markers in human and mouse 
Cell Model Passports  https://cellmodelpassports.sanger.ac.uk  Human cancer cell models 
ChIPprimersDB  http://www.chipprimers.com  qPCR oligonucleotide primers for chromatin immunoprecipitation (ChIP) 
CMAUP  http://bidd2.nus.edu.sg/CMAUP  Collective molecular activities of useful plants 
CoevDB  http://phylodb.unil.ch/CoevDB  Pairwise nucleotide coevolution 
CRISPRlnc  http://crisprlnc.xtbg.ac.cn  Validated CRISPR/Cas9 sgRNAs for model organism lncRNAs 
Cucurbit Genomics Database  http://cucurbitgenomics.org  Genomics of the Cucurbitaceae family 
dbAMP  http://csb.cse.yzu.edu.tw/dbAMP  Antimicrobial peptide sequences, structures and properties 
DSMNC  http://dsmnc.big.ac.cn  Database of somatic mutations in normal cells 
EDK  http://bigd.big.ac.cn/edk  Editome disease knowledgebase 
EncoMPASS  https://encompass.ninds.nih.gov  Encyclopedia of membrane proteins analyzed by structure and symmetry. 
EndoDB  https://vibcancer.be/software-tools/endodb  Gene expression in endothelial cells 
ENPD  http://qinlab.sls.cuhk.edu.hk/ENPD  Eukaryotic nucleic acid binding proteins 
ETCM  http://www.ehbio.com/ETCM  Encyclopedia of Traditional Chinese Medicine 
EVmiRNA  http://bioinfo.life.hust.edu.cn/EVmiRNA  miRNA in extracellular vesicles 
EWAS Atlas  http://bigd.big.ac.cn/ewas  Epigenome-Wide Association Studies 
EWASdb  http://www.bioapp.org/ewas  Epigenome-Wide Association Studies Atlas 
FusionGDB  https://ccsm.uth.edu/FusionGDB  Fusion Gene annotation DataBase 
gcMeta  https://gcmeta.wdcm.org  Microbiome research data 
Genome Properties  https://www.ebi.ac.uk/interpro/genomeproperties  Pathways and other properties represented by sets of protein families 
HACER  http://bioinfo.vanderbilt.edu/AE/HACER  Human ACtive Enhancer to interpret Regulatory variants 
HmtVar  https://www.hmtvar.uniba.it  Human mitochondrial DNA variants 
iDOG  http://bigd.big.ac.cn/idog  Dog data on genes, SNPs, diseases etc. 
iProX  http://www.iprox.org  Proteomics datasets 
jPOSTdb  https://jpostdb.org  Japan ProteOme STandard environment 
KinaMetrix  http://kinametrix.com  Protein kinase models, conformations and ligands 
liqDB  http://bioinfo5.ugr.es/liqdb  Small RNA expression profiles in biofluids 
LncBook  http://bigd.big.ac.cn/lncbook  Human lncRNA knowledgebase 
MemProtMD  http://memprotmd.bioch.ox.ac.uk  Membrane Proteins Embedded in Lipid Bilayers 
MethMotif  http://bioinfo-csi.nus.edu.sg/methmotif  Transcription factor binding motifs coupled with DNA methylation profiles 
NucMap  http://bigd.big.ac.cn/NucMap  Nucleosome positioning map across species 
OncoBase  http://www.oncobase.biols.ac.cn  Regulatory somatic mutations in human cancers 
OpenProt  http://www.openprot.org  Eukaryotic coding potential and proteomes 
Pancan-meQTL  http://bioinfo.life.hust.edu.cn/Pancan-meQTL  Methylation quantitative trait loci in cancer 
PDX Finder  http://www.pdxfinder.org  Patient-derived xenograft models 
PED  http://bigd.big.ac.cn/ped  Plant Editosome Database 
PreMedKB  http://fudan-pgx.org/premedkb  Precision medicine knowledgebase 
piRTarBase  http://cosbi5.ee.ncku.edu.tw/piRTarBase  piRNA targeting sites 
Plasmid Atlas  http://www.patlas.site  Plasmid annotations and metadata 
PLSDB  https://ccb-microbe.cs.uni-saarland.de/plsdb  Plasmid annotations and metadata 
PopHumanScan  https://pophumanscan.uab.cat  Positively selected regions of the human genome 
qPhos  http://qphos.cancerbio.info  Protein phosphorylation dynamics 
RetroRules  http://retrorules.org  Reaction rules for synthetic biology 
RNact  http://rnact.crg.eu  Experimental and predicted protein–RNA interactions in human and mouse 
SAGD  http://bioinfo.life.hust.edu.cn/SAGD  Sex-associated gene database 
SEdb  http://www.licpathway.net/sedb  Super-enhancer database 
SSRome  http://mggm-lab.easyomics.org  Microsatellites in all organisms 
SymMap  http://www.symmap.org  Traditional chinese medicine including symptom mapping 
Translocatome  http://translocatome.linkgroup.hu  Translocating human proteins 
Trips-Viz  http://trips.ucc.ie  Transcriptome browser 
UniLectin  http://www.unilectin.eu  Lectin structure and function 
ViBrism DB  https://vibrism.neuroinf.jp  Tomographic transcriptome and co-expression networks in mouse brain 
Victors  http://www.phidias.us/victors  Virulence factors 
VMH  http://vmh.life  Virtual metabolic human 
YeastRGB  http://www.yeastRGB.org  Expression and localization of yeast proteins 

Table 2. Updated descriptions of databases most recently published elsewhere

Database  URL  Brief description 
CADD  http://cadd.gs.washington.edu  Combined annotation-dependent depletion 
GENCODE  http://www.gencodegenes.org  Reference annotation for the human and mouse genomes. 
glycosciences.DB  http://www.glycosciences.de/database  Glyco-related databases 
Haemopedia  http://haemosphere.org  Haematopoietic expression data 
HumanNet  https://www.inetbio.org/humannet  Human gene functional network 
LncACTdb  http://www.bio-bigdata.net/LncACTdb  lncRNA–miRNA–gene interactions 
MoonDB  http://moondb.hb.univ-amu.fr  Known and predicted multifunctional proteins in model organisms 
OrthoInspector  http://lbgi.fr/orthoinspectorv3  Orthologous relations and phylogenetic profiling 
piRBase  http://www.regulatoryrna.org  piRNA function and annotation 
Stemformatics  http://stemformatics.org  Stem cell and other cell-specific gene expression 
UNITE  https://unite.ut.ee  Internal transcribed spacer sequences for fungal identification 
Vesiclepedia  http://www.microvesicles.org  Extracellular vesicles 

Reference: https://academic.oup.com/nar/article/47/D1/D1/5280358

Souce: Nucleic Acids Research    2019-03-09