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