Table 1.
New online databases featured in the 2013 NAR Database issue
| Database name | URL | Brief description |
|---|---|---|
| APPRIS | http://appris.bioinfo.cnio.es/ | A system for annotating alternative splice isoforms |
| BioLiP | http://zhanglab.ccmb.med.umich.edu/BioLiP/ | Biologically relevant ligand–protein interactions |
| BSRD | http://kwanlab.bio.cuhk.edu.hk/BSRD | A repository of bacterial small regulatory RNA |
| CellLineNavigator | http://www.medicalgenomics.org/celllinenavigator | Cell line expression profiles by microarray analysis |
| ChIPBase | http://deepbase.sysu.edu.cn/chipbase/ | Transcriptional regulation of lncRNA and microRNA genes from ChIP-Seq data |
| ChiTaRS | http://chimerasrch.bioinfo.cnio.es/ | Chimeric RNAs of two or more different transcripts |
| CIL-CCDB | http://www.cellimagelibrary.org/ | Images, videos and animations of various cell types from diverse organisms |
| CircaDB | http://bioinf.itmat.upenn.edu/circa/ | Circadian gene expression profiles in human and mouse |
| CloneDB | http://www.ncbi.nlm.nih.gov/clone/ | Clones and libraries: sequence data, map positions and distributor information |
| ClusterMine360 | http://www.sigma54.ca/microbialclusters/ | Microbial PKS/NRPS Biosynthesis |
| Cyanolyase | http://cyanolyase.genouest.org/ | Sequences and motifs of the phycobilin lyase protein family |
| D2P2 | http://d2p2.pro/ | Database of Disordered Protein Predictions |
| dbVar | http://www.ncbi.nlm.nih.gov/dbvar | Structural variation in chromosomes: inversions, translocations, insertions and deletions |
| DGVa | http://www.ebi.ac.uk/dgva/ | |
| dcGO | http://supfam.org/SUPERFAMILY/dcGO | domain-centric Gene Ontology |
| Dfam | http://dfam.janelia.org | Human DNA repeat families |
| DGA | http://dga.nubic.northwestern.edu/ | Disease and Gene Annotations database |
| DIANA-LncBase | http://www.microrna.gr/LncBase | microRNA targets on long noncoding RNAs |
| DoBISCUIT | http://www.bio.nite.go.jp/pks/ | Database Of BIoSynthesis clusters CUrated and InTegrated |
| EBI Enzyme Portal | http://www.ebi.ac.uk/enzymeportal | Various kinds of information about enzymes: small-molecule chemistry, biochemical pathways and drug compounds |
| ECMDB | http://www.ecmdb.ca/ | Escherichia coli Metabolome Database |
| EENdb | http://eendb.zfgenetics.org/ | Engineered endonucleases: zinc finger nucleases and transcription activator-like effector nucleases |
| eProS | http://bioservices.hs-mittweida.de/Epros/ | Energy profiles of protein structures |
| Factorbook | http://www.factorbook.org/ | Human transcription factor-binding data from ChIP-seq |
| G4LDB | http://www.g4ldb.org/ | G-quadruplex Ligands Database |
| GDSC | http://www.cancerRxgene.org/ | Genomics of Drug Sensitivity in Cancer: Sensitivity for anti-cancer drugs in various cell lines |
| GeneTack | http://topaz.gatech.edu/GeneTack/db.html | Genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences |
| Genome3D | http://genome3d.eu/ | Domain structure predictions and 3D models for proteins from model genomes |
| Glycan Fragment DB | http://www.glycanstructure.org/fragment-db | Database of glycan 3D structures |
| H2DB | http://tga.nig.ac.jp/h2db/ | Heritability data with trait-associated genomic loci |
| HBVdb | http://hbvdb.ibcp.fr/HBVdb/ | A knowledge database for the Hepatitis B Virus |
| HemaExplorer | http://servers.binf.ku.dk/shs/ | Gene expression profiles in haematopoiesis |
| HEXEvent | http://hertellab.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi | Human Exone Splicing Events |
| HOCOMOCO | http://autosome.ru/HOCOMOCO, http://cbrc.kaust.edu.sa/hocomoco/ | HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor-binding site models |
| KIDFamMap | http://gemdock.life.nctu.edu.tw/KIDFamMap/ | Kinase-Inhibitor-Disease Family Map |
| LAMP | http://www.llamp.net/ | Library of Apicomplexan Metabolic Pathways |
| Lncipedia | http://www.lncipedia.org/ | Human lncRNA gene sequences and structures |
| LncRNADisease | http://cmbi.bjmu.edu.cn/lncrnadisease | Long non-coding RNA-associated diseases |
| LUCApedia | http://eeb.princeton.edu/lucapedia/ | Predicted genome of Last Universal Common Ancestor |
| meta.MicrobesOnline | http://meta.MicrobesOnline.org/ | Comparative genomic tools for metagenome analysis |
| MetaboLights | http://www.ebi.ac.uk/metabolights | Metabolomics experiments and associated metadata |
| MetalPDB | http://metalweb.cerm.unifi.it/ | Metal-binding sites in macromolecular structures |
| METscout | http://metscout.mpg.de | Spatial organization of metabolic reactions in the mouse |
| MonarchBase | http://monarchbase.umassmed.edu/ | Genome biology of the monarch butterfly Danaus plexippus |
| NetwoRx | http://ophid.utoronto.ca/networx/ | Chemogenomic experiments in yeast: connection of drug response to biological pathways, phenotypes, and networks |
| NCBI Bookshelf | http://www.ncbi.nlm.nih.gov/books | Free online books on the NCBI website |
| NHPRTR | http://nhprtr.org/ | Non-human Primate Reference Transcriptome Resource |
| NIH Genetic Testing Registry | http://www.ncbi.nlm.nih.gov/gtr/ | Genetic tests and laboratories that perform them |
| NPACT | http://crdd.osdd.net/raghava/npact/ | Naturally occurring Plant-based Anticancer Compound Targets |
| OikoBase | http://oikoarrays.biology.uiowa.edu/Oiko/ | Genome expression database of Oikopleura dioica |
| OrtholugeDB | http://www.pathogenomics.sfu.ca/ortholugedb/ | Microbial orthology resource |
| OrysPSSP | http://genoportal.org/SPD/index.do | Small secreted proteins from rice |
| Papillomavirus Episteme | http://PaVE.niaid.nih.gov/ | A database of Papillomaviridae family of viruses |
| PGDD | http://chibba.agtec.uga.edu/duplication/ | Plant Genome Duplication Database |
| PIECE | http://probes.pw.usda.gov/piece/ | Plant Intron Exon Comparison and Evolution |
| PlantRNA | http://plantrna.ibmp.cnrs.fr/ | tRNAs of plants and algae |
| PR2 | http://ssu-rrna.org/ | Protist Ribosomal reference database |
| prePPI | http://bhapp.c2b2.columbia.edu/PrePPI | Predicted and experimentally determined protein–protein interactions for yeast and human |
| PTMcode | http://ptmcode.embl.de/ | Functional associations between posttranslational modifications within proteins |
| Quorumpeps | http://quorumpeps.ugent.be/ | A database of quorum-sensing peptides |
| RhesusBase | http://www.rhesusbase.org/ | A Knowledgebase for the Monkey Research Community |
| RiceFREND | http://ricefrend.dna.affrc.go.jp/ | Rice Functionally Related gene Expression Network Database |
| RNApathwaysDB | http://rnb.genesilico.pl/ | A database of RNA processing pathways |
| SecReT4 | http://db-mml.sjtu.edu.cn/SecReT4/ | Type IV Secretion system Resource |
| SEVA | http://seva.cnb.csic.es/SEVA/ | Standard European Vector Architecture: a collection of plasmids to analyse complex prokaryotic phenotypes |
| SIFTS | http://www.ebi.ac.uk/pdbe/docs/sifts/ | Structure Integration with Function, Taxonomy and Sequences |
| SINEBase | http://sines.eimb.ru | A database of short interspersed elements (SINEs) |
| SomamiR | http://compbio.uthsc.edu/SomamiR/ | Somatic mutations that impact microRNA targeting in cancer |
| Spermatogenesis Online | http://mcg.ustc.edu.cn/sdap1/spermgenes/ | Spermatogenesis-related genes |
| SpliceAid-F | http://mi.caspur.it/SpliceAidF/ | Human splicing factors and their RNA-binding sites |
| Spliceosome Database | http://spliceosomedb.ucsc.edu/ | Spliceosome genes and proteins, splicing complexes |
| StreptomeDB | http://streptomedb.pharmaceutical-bioinformatics.de | Antibiotic, anti-tumour and immunosuppressant drugs produced by Streptomyces spp. |
| SwissBioisostere | http://www.swissbioisostere.ch/ | Molecular replacements for ligand design |
| SwissSidechain | http://www.swisssidechain.ch/ | Non-natural amino acid sidechains for protein engineering |
| SynSysNet | http://bioinformatics.charite.de/synsysnet/ | Synapse proteins, their structures and interactions |
| TCMID | http://www.megabionet.org/tcmid/ | Traditional Chinese Medicine Integrated Database |
| TFClass | http://www.edgar-wingender.de/huTF_classification.html | Human transcription factors classified according to their DNA-binding domains |
| TissueNet | http://netbio.bgu.ac.il/tissuenet/ | Tissue distribution of protein–protein interactions |
| TOPPR | http://iomics.ugent.be/toppr/ | The Online Protein Processing Resource |
| TSGene | http://bioinfo.mc.vanderbilt.edu/TSGene/ | Tumor Suppressor Gene database |
| UCNEbase | http://ccg.vital-it.ch/UCNEbase/ | Ultraconserved non-coding elements and gene regulatory blocks |
| UUCD | http://uucd.biocuckoo.org/ | Ubiquitin and ubiquitin-like conjugation database |
| ValidNESs | http://validness.ym.edu.tw/ | Validated nuclear export signals-containing proteins |
| Voronoia4RNA | http://proteinformatics.charite.de/voronoia4rna/tools/v4rna/index | Packing of RNA molecules and complexes |
| WDDD | http://so.qbic.riken.jp/wddd/ | Worm Developmental Dynamics Database |
| WholeCellKB | http://wholecellkb.stanford.edu/ | Pathway and genome database of Mycoplasma genitalium for whole-cell modelling |
| WormQTL | http://www.wormqtl.org | Natural variation data in Caenorhabditis spp. |
| YM500 | http://ngs.ym.edu.tw/ym500/ | smRNA-seq database for miRNA research |
| ZInC | http://research.nhgri.nih.gov/zinc | Zebrafish Insertions Collection |