These abbreviations are used in PubMed and refer to Molecular Biology databses.
PCR, qPCR and RT-PCR sequences and primers needed to be alligned through different databses. Today most is done by BLAST on NCBI.
Lieven Gevaert, Bio-ir, RUG 1969
Director Gentaur Database
| 16S and 23S rRNA Mutation Database | 16S and 23S ribosomal RNA mutations | http://www.fandm.edu/Departments/Biology/Databases/RNA.html |
| 16S rRNA database | Multiple sequence alignment of prokaryotic 16S rDNA | http://greengenes.llnl.gov/16S/ |
| 2D-PAGE | Proteome database system for microbial research | http://www.mpiib-berlin.mpg.de/2D-PAGE |
| 3D-GENOMICS | Structural annotations for complete proteomes | http://www.sbg.bio.ic.ac.uk/3dgenomics |
| 3DID | 3D interacting domains: Domain-domain interactions in proteins with known 3D structures | http://3did.embl.de |
| 5S rRNA Database | 5S rRNA sequences | http://biobases.ibch.poznan.pl/5SData/ |
| 5’SAGE | 5′-end serial analysis of gene expression | http://5sage.gi.k.u-tokyo.ac.jp/ |
| AAindex | Physicochemical properties of amino acids | http://www.genome.ad.jp/aaindex/ |
| AANT | Amino acid-nucleotide interaction database | http://aant.icmb.utexas.edu/ |
| AARSDB | Aminoacyl-tRNA synthetase database | http://rose.man.poznan.pl/aars/index.html |
| ABA | Ascidian body atlas: digital 3D model of ascidian development | http://ciona.lab.nig.ac.jp/ascidian_3d_db_demo/ascidian/sample/top.html |
| ABCdb | Archaeal and bacterial ABC transporter database | http://www-abcdb.biotoul.fr |
| ABS | Annotated regulatory binding sites from orthologous promoters | http://genome.imim.es/datasets/abs2005/abs.html |
| ACeDB | C. elegans, S. pombe, and human genomic information | http://www.acedb.org/ |
| ACLAME | A classification of genetic mobile elements | http://aclame.ulb.ac.be/ |
| ACTIVITY | Functional DNA/RNA site activity | http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ |
| ADDA | A database of protein domain classification | http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/ |
| AffinDB | Affinity data for protein-ligand complexes | http://www.agklebe.de/affinity |
| AGD | Ashbya gossypii genome database | http://agd.unibas.ch |
| ALFRED | Allele frequencies and DNA polymorphisms | http://alfred.med.yale.edu/ |
| AllGenes | Human and mouse gene, transcript and protein annotation | http://www.allgenes.org/ |
| ALPSbase | Autoimmune lymphoproliferative syndrome database | http://research.nhgri.nih.gov/alps/ |
| AluGene | Complete Alu map in the human genome | http://alugene.tau.ac.il/ |
| AlzGene | Candidate genes for Alzheimer disease | http://www.alzgene.org |
| aMAZE | http://www.amaze.ulb.ac.be/ | |
| Androgen Receptor Gene Mutations Database | Mutations in the androgen receptor gene | http://www.mcgill.ca/androgendb/ |
| ANTIMIC | Database of natural antimicrobial peptides | http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ |
| AOBase | Antisense oligonucleotide selection and design | http://www.bioit.org.cn/ao/aobase |
| APD | Antimicrobial peptide database | http://aps.unmc.edu/AP/main.php |
| ApiEST-DB | EST sequences from various Apicomplexan parasites | http://www.cbil.upenn.edu/paradbs-servlet |
| AppaDB | A database on the nematode Pristionchus pacificus | http://appadb.eb.tuebingen.mpg.de/ |
| Aptamer database | Small RNA/DNA molecules binding nucleic acids, proteins | http://aptamer.icmb.utexas.edu/ |
| ArchDB | Automated classification of protein loop structures | http://gurion.imim.es/archdb |
| ARED | AU-rich element-containing mRNA database | http://rc.kfshrc.edu.sa/ared |
| Argonaute | Gene regulation by mammalian microRNAs | http://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface |
| ArkDB | Genome databases for farm and other animals | http://www.thearkdb.org/ |
| ArrayExpress | Public collection of microarray gene expression data | http://www.ebi.ac.uk/arrayexpress |
| ASAP | Alternative spliced isoforms | http://bioinfo.mbi.ucla.edu/ASAP/ |
| ASAP | A systematic annotation package for community analysis of E. coli and related genomes | https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm |
| ASC | Active sequence collection: biologically-active peptides | http://bioinformatica.isa.cnr.it/ASC/ |
| ASD | Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb | http://www.ebi.ac.uk/asd |
| ASDB | Alternative splicing database: protein products and expression patterns of alternatively-spliced genes | http://hazelton.lbl.gov/~teplitski/alt |
| ASHESdb | Alternatively spliced human genes by exon skipping | http://sege.ntu.edu.sg/wester/ashes/ |
| ASPD | Artificial selected proteins/peptides database | http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ |
| ASTRAL | Sequences of domains of known structure, selected subsets and sequence-structure correspondences | http://astral.stanford.edu/ |
| ATD | Alternate transcript diversity database | http://www.ebi.ac.uk/atd |
| Atlas of Genetics and Cytogenetics in Oncology and Haematology | Cancer related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases | http://www.infobiogen.fr/services/chromcancer/ |
| Axeldb | Gene expression in Xenopus laevis | http://www.dkfz-heidelberg.de/abt0135/axeldb.htm |
| BacMap | Picture atlas of annotated bacterial genomes | http://wishart.biology.ualberta.ca/BacMap |
| BacTregulators | Transcriptional regulators of AraC and TetR families | http://www.bactregulators.org/ |
| BAliBASE | A database for comparison of multiple sequence alignments | http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html |
| BayGenomics | Genes relevant to cardiovascular and pulmonary disease | http://baygenomics.ucsf.edu/ |
| BeetleBase | Genome database of the beetle Tribolium castaneum | http://www.bioinformatics.ksu.edu/BeetleBase/ |
| BGED | Brain gene expression database | http://genome.mc.pref.osaka.jp/BGED/ |
| BIND | http://www.bind.ca | |
| BioCarta | http://www.biocarta.com/genes/allPathways.asp | |
| BioCyc | Pathway/genome databases for many bacteria | http://biocyc.org/ |
| BioGrid | http://biodata.mshri.on.ca/grid | |
| BioImage | Database of multidimensional biological images | http://www.bioimage.org/ |
| BioMagResBank | NMR spectroscopic data for proteins and nucleic acids | http://www.bmrb.wisc.edu/ |
| BioModels | Published mathematical models of biological interest | http://www.ebi.ac.uk/biomodels/ |
| BioSilico | Integrated access to various metabolic databases | http://biosilico.kaist.ac.kr/ |
| BIOZON | A database of gene and protein familiy classification | http://biozon.org |
| Blocks | Alignments of conserved regions in protein families | http://blocks.fhcrc.org/ |
| BodyMap | Human and mouse gene expression data | http://bodymap.ims.u-tokyo.ac.jp/ |
| BodyMap-Xs | A database for cross-species comparison of vertebrate gene expression | http://bodymap.jp/ |
| BRENDA | Enzyme names and biochemical properties | http://www.brenda.uni-koeln.de |
| BRITE | http://www.genome.ad.jp/brite | |
| BSD | Biodegradative strain database: Microorganisms that can degrade aromatic and other organic compounds | http://bsd.cme.msu.edu/ |
| BSORF | Bacillus subtilis genome database at Kyoto U. | http://bacillus.genome.ad.jp/ |
| BTKbase | Mutation registry for X-linked agammaglobulinemia | http://bioinf.uta.fi/BTKbase/ |
| C. elegans Project | Genome sequencing data at the Sanger Institute | http://www.sanger.ac.uk/Projects/C_elegans |
| CADB | Conformational angles in proteins database | http://cluster.physics.iisc.ernet.in/cadb/ |
| CADRE | Central Aspergillus data repository | http://www.cadre.man.ac.uk/ |
| CAGE | CAGE tags for cap-analysis of gene expression | http://fantom31p.gsc.riken.jp/cage/mm5/ |
| CampyDB | Database for Campylobacter genome analysis | http://campy.bham.ac.uk/ |
| Cancer Chromosomes | Cytogenetic, clinical, and reference information on cancer-related aberrations | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes |
| Candida Genome | Candida albicans genome database | http://www.candidagenome.org/ |
| CandidaDB | Candida albicans genome database | http://genolist.pasteur.fr/CandidaDB |
| CarpeDB | Comprehensive database on the genetics of epilepsy | http://www.carpedb.ua.edu/ |
| CASRDB | Calcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism | http://www.casrdb.mcgill.ca/ |
| CATH | Protein domain structures database | http://www.biochem.ucl.ac.uk/bsm/cath_new |
| CCDS | Consensus CDS: collaborative effort to identify a core set of human protein coding regions | http://www.ncbi.nlm.nih.gov/projects/CCDS/ |
| CCSD | Complex carbohydrate structure database (CarbBank ) | http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm |
| CDD | Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases | http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml |
| CE | 3D protein structure alignments | http://cl.sdsc.edu/ce.html |
| CGED | Cancer gene expression database | http://cged.hgc.jp |
| ChEBI | Chemical entities of biological interest | http://www.ebi.ac.uk/chebi/ |
| ChickVD | Sequence variation in the chicken genome | http://chicken.genomics.org.cn/ |
| ChimerDB | Putative chimeric sequences in the GenBank | http://genome.ewha.ac.kr/ECgene/ChimerSearch/ |
| CIDB | Chlamydia Interactive Database: Gene expression data | http://www.it.deakin.edu.au/CIDB |
| Ciliate IES-MDS Db | Macro- and micronuclear genes in spirotrichous ciliates | http://oxytricha.princeton.edu/dimorphism/database.htm |
| CisRed | Human regulatory DNA sequence motifs | http://www.cisred.org/ |
| CKAAPs DB | Structurally-similar proteins with dissimilar sequences | http://ckaap.sdsc.edu/ |
| CleanEx | Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons | http://www.cleanex.isb-sib.ch/ |
| ClostriDB | Finished and unfinished genomes of Clostridium spp. | http://clostri.bham.ac.uk/ |
| CluSTr | Clusters of Swiss-Prot+TrEMBL proteins | http://www.ebi.ac.uk/clustr |
| CnidBase | Cnidarian evolution and gene expression database | http://cnidbase.bu.edu/ |
| CoC | Conservation of conservation: Universally conserved residues in selected protein folds | http://kulibin.mit.edu/coc/ |
| COG | Clusters of orthologous groups of proteins | http://www.ncbi.nlm.nih.gov/COG |
| COGEME | Phytopathogenic fungi and oomycete EST database | http://cogeme.ex.ac.uk |
| CoGenT++ | Complete genome tracking: Predicted peptides from fully sequenced genomes | http://cgg.ebi.ac.uk/cogentpp.html |
| coliBase | A database for E. coli, Salmonella and Shigella | http://colibase.bham.ac.uk/ |
| Colibri | E. coli genome database at Institut Pasteur | http://genolist.pasteur.fr/Colibri/ |
| Collagen Mutation Database | Human type I and type III collagen gene mutations | http://www.le.ac.uk/genetics/collagen/ |
| Columba | Annotation of protein structures from the PDB | http://www.columba-db.de |
| COMe | Co-ordination of metals etc.: classification of metalloproteins | http://www.ebi.ac.uk/come |
| Comparative Genometrics | Nucleotide frequencies and the GC and TA skews in complete genome sequences | http://www.unil.ch/comparativegenometrics/ |
| CopS | Comprehensive peptide signature database | http://203.90.127.70/copsv2/index.html |
| CORG | Comparative regulatory genomics: conserved non-coding sequence blocks | http://corg.molgen.mpg.de/ |
| COSMIC | Catalogue of somatic mutations in cancer: Sequence data, samples and publications | http://www.sanger.ac.uk/perl/CGP/cosmic |
| Cre Transgenic Database | Cre transgenic mouse lines with links to publications | http://www.mshri.on.ca/nagy/ |
| CroW 21 | Human chromosome 21 database | http://bioinfo.weizmann.ac.il/crow21/ |
| CryptoDB | Cryptosporidium parvum genome database | http://cryptodb.org/ |
| CSA | Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure | http://www.ebi.ac.uk/thornton-srv/databases/CSA/ |
| CSD | Cambridge structural database: Crystal structure information for organic and metal-organic compounds | http://www.ccdc.cam.ac.uk/prods/csd/csd.html |
| CSDBase | Cold shock domain-containing proteins | http://www.chemie.uni-marburg.de/~csdbase/ |
| CSS | Carbohydrate structure suite: carbohydrate 3D structures | http://www.dkfz.de/spec/css/ |
| CTGA | The catalogue for transmission genetics in Arabs | http://www.cags.org.ae |
| CUTG | Codon usage tabulated from GenBank | http://www.kazusa.or.jp/codon/ |
| CuticleDB | Structural proteins of Arthropod cuticle | http://bioinformatics.biol.uoa.gr/cuticleDB |
| CyanoBase | Cyanobacterial genomes | http://www.kazusa.or.jp/cyano |
| Cybase | Proteins with cyclic backbones | http://research.imb.uq.edu.au/cybase/html/index.php |
| CyberCell database | A collection of data on E. coli K12 intended for mathematical modeling to simulate the bacterial cell | http://redpoll.pharmacy.ualberta.ca/CCDB |
| Cyclonet | http://cyclonet.biouml.org/index.html | |
| CYGD | MIPS Comprehensive yeast genome database | http://mips.gsf.de/proj/yeast |
| Cypriot national mutation database | Disease mutations in the Cypriot population | http://www.goldenhelix.org/cypriot/ |
| Cytokine Gene Polymorphism in Human Disease | Cytokine gene polymorphism literature database | http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm |
| Dali | Protein fold classification using the Dali search engine | http://www.bioinfo.biocenter.helsinki.fi:8080/dali/ |
| DART | Drug adverse reaction target database | http://xin.cz3.nus.edu.sg/group/drt/dart.asp |
| Database name | Full name and/or description | URL |
| Database of Genomic Variants | Human genomic variants: frequency, segmental duplications and genome assembly gaps | http://projects.tcag.ca/variation/ |
| DBD | Transcription factor prediction database | http://stash.mrc-lmb.cam.ac.uk/skk/Cell2/index.cgi?Home |
| dbERGEII | Database of experimental results on gene expression: Genomic alignment, annotation and experimental data | http://dberge.cse.psu.edu/menu.html |
| dbPTM | Information on post-translational modification of proteins | http://dbptm.mbc.nctu.edu.tw/ |
| dbQSNP | Quantification of SNP allele frequencies database | http://qsnp.gen.kyushu-u.ac.jp/ |
| dbRIP | Human retrotransposon insertion polymorphism | http://falcon.roswellpark.org:9090/ |
| dbSNP | Database of single nucleotide polymorphisms | http://www.ncbi.nlm.nih.gov/SNP/ |
| DBSubLoc | Database of protein subcellular localization | http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html |
| DBTBS | Bacillus subtilis promoters and transcription factors | http://dbtbs.hgc.jp/ |
| DBTGR | A database of tunicate (Ciona) gene regulation | http://dbtgr.hgc.jp/ |
| DCCP | Database of copper-chelating proteins | http://sdbi.sdut.edu.cn/DCCP/en/index.php |
| DDBJ – DNA Data Bank of Japan | All known nucleotide and protein sequences | http://www.ddbj.nig.ac.jp |
| DDIB | Database of domain interactions and binding | http://www.ddib.org/ |
| Decoys ‘R’ Us | Computer-generated protein conformations | http://dd.stanford.edu/ |
| DED | Database of evolutionary distances | http://warta.bio.psu.edu/DED/ |
| DEG | Database of essential genes from bacteria and yeast | http://tubic.tju.edu.cn/deg |
| Deniz | Beta-thalassemia allele frequencies in world populations | http://biobase.fatih.edu.tr/deniz1.html |
| DExH/D Family Database | DEAD-box, DEAH-box and DExH-box proteins | http://www.helicase.net/dexhd/dbhome.htm |
| DG-CST | Disease gene conserved sequence tags | http://143.225.208.11/cst3/ |
| Diatom EST Database | ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum | http://avesthagen.sznbowler.com/ |
| DictyBase | Universal resource for Dictyostelium discoideum | http://dictybase.org/ |
| DIP | Database of interacting proteins: Experimentally-determined protein-protein interactions | http://dip.doe-mbi.ucla.edu |
| DisProt | Database of Protein Disorder: proteins that lack fixed 3D structure in their native states | http://divac.ist.temple.edu/disprot |
| DMAPS | A database of multiple alignments for protein structures | http://bioinformatics.albany.edu/~dmaps |
| DomIns | Domain insertions in known protein structures | http://www.domins.org/ |
| DoOP | Database of orthologous promoters: chordates and plants | http://doop.abc.hu/ |
| DPDB | Drosophila polymorphism database | http://dpdb.uab.es/ |
| DPInteract | Binding sites for E. coli DNA-binding proteins | http://arep.med.harvard.edu/dpinteract |
| DPVweb | Descriptions of plant viruses | http://www.dpvweb.net |
| DRC | Database of ribosomal crosslinks | http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc |
| Drosophila microarray project | Data and tools for Drosophila gene expression studies | http://www.flyarrays.com/fruitfly |
| DrugBank | Combined information on drugs and drug targets | http://redpoll.pharmacy.ualberta.ca/drugbank/ |
| DSDBASE | Native and modeled disulfide bonds in proteins | http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html |
| DSMM | Database of simulated molecular motions | http://projects.villa-bosch.de/dbase/dsmm/ |
| DynaProt 2D | Proteome database of Lactococcus lactis | http://www.wzw.tum.de/proteomik/lactis/ |
| EASED | Extended alternatively spliced EST database | http://eased.bioinf.mdc-berlin.de/ |
| EBI Genomes | EBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes | http://www.ebi.ac.uk/genomes |
| eBLOCKS | Highly conserved protein sequence blocks | http://fold.stanford.edu/eblocks/acsearch.html |
| ECgene | Genome annotation for alternative splicing | http://genome.ewha.ac.kr/ECgene/ |
| EchoBASE | Post-genomic studies of Escherichia coli | http://www.ecoli-york.org/ |
| EcoCyc | E. coli K12 genes, metabolic pathways, transporters, and gene regulation | http://ecocyc.org/ |
| EcoGene | Sequence and literature data on E. coli genes and proteins | http://bmb.med.miami.edu/EcoGene/EcoWeb/ |
| EDAS | EST-derived alternative splicing database | http://www.ig-msk.ru:8005/EDAS/ |
| eF-site | Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites | http://ef-site.protein.osaka-u.ac.jp/eF-site |
| EGO | Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices | http://www.tigr.org/tdb/tgi/ego/ |
| EHCO | Encyclopedia of hepatocellular carcinoma genes online | http://ehco.nchc.org.tw |
| EICO DB | Expression-based imprint candidate organiser: a database for discovery of novel imprinted genes | http://fantom2.gsc.riken.jp/EICODB/ |
| EID | Exon-intron database | http://www.meduohio.edu/bioinfo/eid/ |
| EMAGE | Edinburgh mouse atlas gene expression database | http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html |
| emap Atlas | Edinburgh mouse atlas: a digital atlas of mouse embryo development and spatially-mapped gene expression | http://genex.hgu.mrc.ac.uk/ |
| EMBL Nucleotide Sequence Database | All known nucleotide and protein sequences | http://www.ebi.ac.uk/embl.html |
| EMGlib | Enhanced microbial genomes library: Completely sequenced genomes of unicellular organisms | http://pbil.univ-lyon1.fr/emglib/emglib.html |
| eMOTIF | Protein sequence motif determination and searches | http://motif.stanford.edu/emotif |
| E-MSD | EBI’s macromolecular structure database | http://www.ebi.ac.uk/msd |
| Endogenous GPCR List | G protein-coupled receptors; expression in cell lines | http://www.tumor-gene.org/GPCR/gpcr.html |
| EndoNet | http://endonet.bioinf.med.uni-goettingen.de/ | |
| Ensembl | Annotated information on eukaryotic genomes | http://www.ensembl.org/ |
| Ensembl | Annotated information on eukaryotic genomes | http://www.ensembl.org/ |
| Entrez Gene | Gene-centered information at NCBI | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene |
| Entrez Genomes | NCBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome |
| ENZYME | Enzyme nomenclature and properties | http://www.expasy.org/enzyme |
| Enzyme Nomenclature | IUBMB Nomenclature Committee recommendations | http://www.chem.qmw.ac.uk/iubmb/enzyme |
| EPConDB | Endocrine pancreas consortium database | http://www.cbil.upenn.edu/EPConDB |
| EPD | Eukaryotic promoter database | http://www.epd.isb-sib.ch |
| EpoDB | Genes expressed during human erythropoiesis | http://www.cbil.upenn.edu/EpoDB/ |
| ERGDB | Estrogen responsive genes database | http://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/ |
| ERGOLight | Integrated biochemical data on 9 bacterial genomes: Publicly-available portion of the ERGO database | http://www.ergo-light.com/ERGO |
| EROP-Moscow | Endogenous regulatory oligopeptide database | http://erop.inbi.ras.ru |
| Essential genes in E. coli | First results of an E. coli gene deletion project | http://www.genome.wisc.edu/resources/essential.htm |
| ESTHER | Esterases and other alpha/beta hydrolase enzymes | http://www.ensam.inra.fr/esther |
| European rRNA database | All complete or nearly complete rRNA sequences | http://www.psb.ugent.be/rRNA/. |
| ExInt | Exon–intron structure of eukaryotic genes | http://sege.ntu.edu.sg/wester/exint/ |
| EXProt | Sequences of proteins with experimentally verified function | http://www.cmbi.kun.nl/EXProt/ |
| Extra-TRAIN | Extragenic regions and transcriptional regulators in bacteria and archaea | http://www.era7.com/ExtraTrain/ |
| EyeSite | Families of proteins functioning in the eye | http://eyesite.cryst.bbk.ac.uk/ |
| EzCatDB | Enzyme Catalytic Mechanism Database | http://mbs.cbrc.jp/EzCatDB/ |
| FANTOM | Functional annotation of mouse full-length cDNA clones | http://fantom3.gsc.riken.jp/ |
| FESD | Functional element SNPs database: SNPs located within promoters, UTRs, etc., of human genes | http://combio.kribb.re.kr/ksnp/resd/ |
| FGDB | MIPS Fusarium graminearum genome database | http://mips.gsf.de/genre/proj/fusarium/ |
| FLIGHT | Inegrated data on Drosophila phenotypes, gene expression and protein interaction data | http://flight.licr.org/ |
| FlyBase | Drosophila sequences and genomic information | http://flybase.bio.indiana.edu/ |
| FlyBrain | Database of the Drosophila nervous system | http://flybrain.neurobio.arizona.edu |
| FlyMine | Integration of insect genomic and proteomic data | http://www.flymine.org/ |
| FlyRNAi DRSC | Genome-wide RNAi analysis data in Drosophila | http://flyRNAi.org/cgi-bin/RNAi_screens.pl |
| FlyTrap | Drosophila mutants created using protein trap strategy | http://flytrap.med.yale.edu/ |
| FlyView | Drosophila development and genetics | http://pbio07.uni-muenster.de/ |
| FREP | Functional repeats in mouse cDNAs | http://facts.gsc.riken.go.jp/FREP/ |
| FSN | Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool | http://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl |
| Full-Malaria | Full-length cDNA library from erythrocytic-stage Plasmodium falciparum | http://fullmal.ims.u-tokyo.ac.jp/ |
| FUNPEP | Low-complexity peptides capable of forming amyloid plaque | http://www.cmbi.kun.nl/swift/FUNPEP/gergo/ |
| FunShift | Functional divergence between the subfamilies of a protein domain family | http://funshift.cgb.ki.se/ |
| FusionDB | Database of bacterial and archaeal gene fusion events | http://igs-server.cnrs-mrs.fr/FusionDB |
| GadFly | Genome annotation database of Drosophila | http://www.fruitfly.org |
| GALA | Genomic alignment, annotation and experimental results | http://gala.cse.psu.edu/ |
| GDB | Human genes and genomic maps | http://www.gdb.org/ |
| GelBank | 2D gel electrophoresis patterns of proteins from complete microbial genomes | http://gelbank.anl.gov/ |
| GenAtlas | Human genes, markers and phenotypes | http://www.genatlas.org/ |
| GenBank® | All known nucleotide and protein sequences | http://www.ncbi.nlm.nih.gov/Entrez |
| GenDiS | Genomic distribution of protein structural superfamilies | http://caps.ncbs.res.in/gendis/home.html |
| Gene Resource Locator | Alignment of ESTs with finished human sequence | http://grl.gi.k.u-tokyo.ac.jp/ |
| Gene3D | Precalculated structural assignments for whole genomes | http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ |
| GeneAnnot | Revised annotation of Affymetrix human gene probe sets | http://genecards.weizmann.ac.il/geneannot/ |
| GeneCards | Integrated database of human genes, maps, proteins and diseases | http://bioinfo.weizmann.ac.il/cards/ |
| GeneDB | Curated database for various Sanger-sequenced genomes | http://www.genedb.org/ |
| GeneLoc | Gene location database | http://genecards.weizmann.ac.il/geneloc/ |
| GeneNest | Gene indices of human, mouse, zebrafish, etc. | http://genenest.molgen.mpg.de/ |
| GeneNet | http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet | |
| GeneNote | Human genes expression profiles in healthy tissues | http://genecards.weizmann.ac.il/genenote/ |
| GenePaint | Gene expression patterns in the mouse | http://www.genepaint.org/Frameset.html |
| Genetic Codes | Genetic codes in various organisms and organelles | http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi |
| GeneTide | A transcriptome-focused member of the GeneCards suite | http://genecards.weizmann.ac.il/genetide/ |
| GeneTrap | Expression patterns in an embryonic stem library of gene trap insertions | http://www.cmhd.ca/genetrap/ |
| Genew | Human gene nomenclature: approved gene symbols | http://www.gene.ucl.ac.uk/nomenclature |
| GeniSys | Enhancer- and promoter-inserted mutants of Drosophila | http://genisys.kaist.ac.kr:8080/ |
| GenMapDB | Mapped human BAC clones | http://genomics.med.upenn.edu/genmapdb |
| GenoBase | E. coli genome database at Nara Institute | http://ecoli.aist-nara.ac.jp/ |
| Génolevures | A comparison of S. cerevisiae and 14 other yeast species | http://cbi.labri.fr/Genolevures |
| Genome Atlas | DNA structural properties of sequenced genomes | http://www.cbs.dtu.dk/services/GenomeAtlas/ |
| Genome Information Broker | DDBJ’s collection of genome databases | http://gib.genes.nig.ac.jp |
| Genome Reviews | Integrated view of complete genomes | http://www.ebi.ac.uk/GenomeReviews/ |
| GenProtEC | E. coli K12 genome and proteome database | http://genprotec.mbl.edu |
| GENSAT | Gene expression nervous system atlas: a map of gene expression in the central nervous system of the mouse | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat |
| GEO | Gene expression omnibus: Gene expression profiles | http://www.ncbi.nlm.nih.gov/geo/ |
| Germline p53 Mutations | Mutations in human tumor and cell line p53 gene | http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm |
| GermOnline | Gene expression in mitotic and meiotic cell cycle | http://www.germonline.org/ |
| GLIDA | G-protein coupled receptors ligand database | http://gdds.pharm.kyoto-u.ac.jp:8081/glida/ |
| Glycan | Carbohydrate database, part of the KEGG system | http://glycan.genome.ad.jp/ |
| GlycoSuiteDB | N- and O-linked glycan structures and biological sources | https://tmat.proteomesystems.com/glycosuite/ |
| GO | Gene ontology consortium database | http://www.geneontology.org/ |
| GOA | EBI’s gene ontology annotation project | http://www.ebi.ac.uk/GOA |
| GOLD | Genomes online database: a listing of completed and ongoing genome projects | http://www.genomesonline.org/ |
| GOLD.db | Genomics of lipid-associated disorders database | http://gold.tugraz.at |
| GPCRDB | G protein-coupled receptors database | http://www.gpcr.org/7tm/ |
| gpDB | G-proteins and their interaction with GPCRs | http://bioinformatics.biol.uoa.gr/gpDB |
| GRAP | Mutants of G-protein coupled receptors of family A | http://tinygrap.uit.no/GRAP/ |
| GRSDB | G-rich sequences database | http://bioinformatics.ramapo.edu/grsdb/ |
| GTD | Genomic threading database: Structural annotations of complete proteomes | http://bioinf.cs.ucl.ac.uk/GTD |
| GTOP | Protein fold predictions from genome sequences | http://spock.genes.nig.ac.jp/~genome/ |
| GtRDB | Genomic tRNA database | http://lowelab.ucsc.edu/GtRNAdb/ |
| Guide RNA Database | RNA editing in various kinetoplastid species | http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html |
| GXD | Mouse gene expression database | http://www.informatics.jax.org/menus/expression_menu.shtml |
| HaemB | Factor IX gene mutations, insertions and deletions | http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html |
| HAGR | Human ageing genomic resources: Genes related to ageing in humans and model organisms | http://genomics.senescence.info/ |
| H-ANGEL | Human anatomic gene expression library | http://www.jbirc.aist.go.jp/hinv/index.jsp |
| HbVar | Human hemoglobin variants and thalassemias | http://globin.cse.psu.edu/globin/hbvar |
| HCAD | Human chromosome aberration database: Chromosomal breakpoints and affected genes | http://www.pdg.cnb.uam.es/UniPub/HCAD/ |
| HCVDB | The hepatitis C virus database | http://hepatitis.ibcp.fr/ |
| HemBase | Genes expressed in differentiating human erythroid cells | http://hembase.niddk.nih.gov/ |
| HemoPDB | Hematopoietic promoter database | http://bioinformatics.med.ohio-state.edu/HemoPDB |
| HERVd | Human endogenous retrovirus database | http://herv.img.cas.cz |
| Het-PDB Navi | Hetero-atoms in protein structures | http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html |
| HGMD | Human gene mutation database | http://www.hgmd.org/ |
| HGT-DB | Putative horizontally-transferred genes in prokaryotic genomes | http://www.fut.es/~debb/HGT/ |
| HGVbase | Human genome variation database: Curated human polymorphisms | http://hgvbase.cgb.ki.se/ |
| HGVS Databases | A compilation of human mutation databases | http://www.hgvs.org/ |
| HIC-Up | Hetero-compound Information Centre – Uppsala | http://xray.bmc.uu.se/hicup |
| H-InvDB | Full-length human cDNA clones | http://www.h-invitational.jp/ |
| Histone Database | Histone fold sequences and structures | http://research.nhgri.nih.gov/histones/ |
| Hits | A database of protein domains and motifs | http://hits.isb-sib.ch/ |
| HIV Drug Resistance Database | HIV mutations that confer resistance to anti-HIV drugs | http://resdb.lanl.gov/Resist_DB/default.htm |
| HIV Molecular Immunology Database | HIV epitopes | http://hiv-web.lanl.gov/immunology/ |
| HIV RT and Protease Sequence Database | HIV reverse transcriptase and protease sequences | http://hivdb.stanford.edu/ |
| HIV Sequence Database | HIV RNA sequences | http://hiv-web.lanl.gov/ |
| Hollywood | Exon annotation database | http://hollywood.mit.edu |
| Homeobox Page | Homeobox proteins, classification and evolution | http://www.biosci.ki.se/groups/tbu/homeo.html |
| Homeodomain Resource | Homeodomain sequences, structures and related genetic and genomic information | http://research.nhgri.nih.gov/homeodomain/ |
| HomoloGene | Automatically detected homologous genes in complete eukaryotic genomes | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene |
| Homophila | Drosophila homologs of human disease genes to | http://superfly.ucsd.edu/homophila/ |
| HOMSTRAD | Homologous structure alignment database: curated structure-based alignments for protein families | http://www-cryst.bioc.cam.ac.uk/homstrad |
| Hoppsigen | Human and mouse homologous processed pseudogenes | http://pbil.univ-lyon1.fr/databases/hoppsigen.html |
| HORDE | Human olfactory receptor data exploratorium | http://bioinfo.weizmann.ac.il/HORDE/ |
| HOWDY | Human organized whole genome database | http://www-alis.tokyo.jst.go.jp/HOWDY/ |
| Hox-Pro | Homeobox genes database | http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html |
| hp-DPI | Database of protein interactions in Helicobacter pylori | http://dpi.nhri.org.tw/hp/ |
| HPID | Human protein interaction database | http://www.hpid.org/ |
| HPMR | Human plasma membrane receptome: sequences, literature, and expression data | http://receptome.stanford.edu/ |
| HPRD | Human protein reference database: domain architecture, post-translational modifications, and disease association | http://www.hprd.org |
| HPTAA | Human potential tumor-associated antigens | http://www.bioinfo.org.cn/hptaa/ |
| HS3D | Homo sapiens splice sites dataset | http://www.sci.unisannio.it/docenti/rampone/ |
| HTPSELEX | Transcription factor binding site sequences obtained using high-throughput SELEX method | http://www.isrec.isb-sib.ch/htpselex/ |
| HUGE | Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences | http://www.kazusa.or.jp/huge |
| HugeIndex | Expression levels of human genes in normal tissues | http://zlab.bu.edu/HugeSearch |
| HuGeMap | Human genome genetic and physical map data | http://www.infobiogen.fr/services/Hugemap |
| Human BAC Ends | Non-redundant human BAC end sequences | http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html |
| Human Genome Segmental Duplication Database | Segmental duplications in the human genome | http://projects.tcag.ca/humandup |
| Human p53/hprt, rodent lacI/lacZ databases | Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations | http://www.ibiblio.org/dnam/mainpage.html |
| Human PAX2 Allelic Variant Database | Mutations in human PAX2 gene | http://pax2.hgu.mrc.ac.uk/ |
| Human PAX6 Allelic Variant Database | Mutations in human PAX6 gene | http://pax6.hgu.mrc.ac.uk/ |
| HumHot | Human meiotic recombination hot spots | http://www.jncasr.ac.in/humhot/ |
| HUNT | Human novel transcripts: annotated full-length cDNAs | http://www.hri.co.jp/HUNT |
| HuSiDa | Human siRNA database | http://itb1.biologie.hu-berlin.de/~nebulus/sirna/ |
| HyPaLib | Hybrid pattern library: structural elements in classes of RNA | http://bibiserv.techfak.uni-bielefeld.de/HyPa/ |
| IARC TP53 Database | Human TP53 somatic and germline mutations | http://www-p53.iarc.fr/index.html |
| ICB | gyrB database for identification of bacteria | http://seasquirt.mbio.co.jp/icb/index.php |
| ICDS | Interrupted coding sequences – frameshifts, stop codons, sequencing errors in microbial genomes | http://www-bio3d-igbmc.u-strasbg.fr/ICDS/ |
| IGTC | International mouse Gene Trap Consortium data | http://wwwtest.genetrap.org |
| IMB Jena Image Library | Visualization and analysis of 3D biopolymer structures | http://www.imb-jena.de/IMAGE.html |
| IMG | Intergrated microbial genome database at the DOE Joint Genome Institute | http://img.jgi.doe.gov/ |
| IMGT/3Dstructure-DB | Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins | http://imgt3d.igh.cnrs.fr/ |
| IMGT/PRIMER-DB | Immunogenetics oligonucleotide primer database | http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl |
| IMOTdb | Spatially interacting motif database | http://caps.ncbs.res.in/imotdb/ |
| Imprinted Gene Catalogue | Imprinted genes and parent-of-origin effects in animals | http://igc.otago.ac.nz/home.html |
| InBase | Inteins (protein splicing elements) database: properties, sequences, bibliography | http://www.neb.com/neb/inteins.html |
| INFEVERS | Hereditary inflammatory disorder and familial mediterranean fever mutation data | http://fmf.igh.cnrs.fr/infevers |
| Influenza Virus Resource | Protein and nucleotide sequences of the influenza virus | http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html |
| Inparanoid | A database of eukaryotic orthologs | http://inparanoid.cgb.ki.se/ |
| InsulatorDB | Insulator regulatory elements in vertebrate genomes | http://insulatordb.utmem.edu |
| IntAct project | Protein-protein interaction data | http://www.ebi.ac.uk/intact |
| Integr8 | Functional classification of proteins in whole genomes | http://www.ebi.ac.uk/integr8/ |
| IntEnz | Integrated enzyme database and enzyme nomenclature | http://www.ebi.ac.uk/intenz |
| InterActive Fly | Drosophila genes and their roles in development | http://flybase.bio.indiana.edu/allied-data/lk/interactive-fly/aimain/1aahome.htm |
| Inter-Chain Beta-Sheets | Protein-protein interactions mediated by interchain beta-sheet formation | http://www.igb.uci.edu/servers/icbs/ |
| InterDom | Putative protein domain interactions | http://interdom.lit.org.sg |
| InterPro | Integrated resource of protein families, domains and functional sites | http://www.ebi.ac.uk/interpro |
| Intronerator | Alternative splicing in C. elegans and C. briggsae | http://www.cse.ucsc.edu/~kent/intronerator/ |
| Intronerator | Introns and splicing in C. elegans and C. briggsae | http://www.cse.ucsc.edu/~kent/intronerator/ |
| INVHOGEN | Homologous invertebrate genes | http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html |
| IPD | Immuno polymorphism database | http://www.ebi.ac.uk/ipd |
| IPI | International protein index: human, mouse and rat proteins | http://www.ebi.ac.uk/IPI |
| iProClass | Integrated protein classification database | http://pir.georgetown.edu/iproclass/ |
| iProClass | Protein families defined by PIR superfamilies and PROSITE patterns | http://pir.georgetown.edu/gfserver/proclass.html |
| IRESdb | Internal ribosome entry site database | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ |
| IRESite | Experimentally studied internal ribosome entry sites | http://www.iresite.org/ |
| ISfinder | Insertion sequences from bacteria and archaea | http://www-is.biotoul.fr |
| Islander | Pathogenicity islands and prophages in bacterial genomes | http://www.indiana.edu/~islander |
| ISSD | Integrated sequence-structure database | http://www.protein.bio.msu.su/issd |
| ITTACA | Integrated tumor transcriptome array and clinical data analysis | http://bioinfo.curie.fr/ittaca |
| IUBMB Nomenclature database | Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins | http://www.chem.qmul.ac.uk/iubmb |
| IUPAC Nomenclature database | Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission | http://www.chem.qmul.ac.uk/iupac |
| IUPHAR-RD | International Union of Pharmacology recommendations on receptor nomenclature and drug classification | http://www.iuphar-db.org/iuphar-rd/ |
| IXDB | Physical maps of human chromosome X | http://ixdb.mpimg-berlin-dahlem.mpg.de/ |
| JASPAR | PSSMs for transcription factor DNA-binding sites | http://jaspar.cgb.ki.se |
| JSNP | Japanese SNP database | http://snp.ims.u-tokyo.ac.jp/ |
| KaryotypeDB | Karyotype and chromosome data for animal and plant species | http://www.nenno.it/karyotypedb/ |
| KDBI | Kinetic data of bio-molecular interactions | http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php |
| KEGG | Kyoto encyclopedia of genes and genomes: databases on genes, proteins, and metabolic pathways | http://www.genome.jp/kegg |
| KEGG Pathway | Metabolic and regulatory pathways in complete genomes | http://www.genome.jp/kegg/pathway.html |
| Kidney Development Database | Kidney development and gene expression | http://golgi.ana.ed.ac.uk/kidhome.html |
| KinG – Kinases in Genomes | S/T/Y-specific protein kinases encoded in complete genomes | http://hodgkin.mbu.iisc.ernet.in/~king |
| KinMutBase | Disease-causing protein kinase mutations | http://www.uta.fi/imt/bioinfo/KinMutBase/ |
| Klotho | Collection and categorization of biological compounds | http://www.biocheminfo.org/klotho |
| Knottins | Database of knottins – small proteins with an unusual “disulfide through disulfide” knot | http://knottin.cbs.cnrs.fr |
| KOG | Eukaryotic orthologous groups of proteins | http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi |
| L1Base | Functional annotation and prediction of LINE-1 elements | http://line1.molgen.mpg.de/ |
| LEGER | Post-genome research of Listeria | http://leger2.gbf.de/cgi-bin/expLeger.pl |
| LeptoList | Leptospira interrogans genome | http://bioinfo.hku.hk/LeptoList |
| LGICdb | Ligand-gated ion channel subunit sequences database | http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html |
| LIFEdb | Localization, interaction and functions of human proteins | http://www.dkfz.de/LIFEdb |
| LIGAND | Chemical compounds and reactions in biological pathways | http://www.genome.ad.jp/ligand/ |
| Lipase Engineering Database | Sequence, structure and function of lipases and esterases | http://www.led.uni-stuttgart.de/ |
| Lipid MAPS | Lipid metabolites and pathways strategy | http://www.lipidmaps.org |
| LOCATE | Membrane organization and subcellular localization of mouse proteins | http://mpdb.imb.uq.edu.au |
| LOLA | List of lists annotated: a comparison of gene sets identified in different microarray experiments | http://www.lola.gwu.edu/ |
| Lowe Syndrome Mutation Database | Mutations causing Lowe oculocerebrorenal syndrome | http://research.nhgri.nih.gov/lowe/ |
| LOX-DB | Mammalian, invertebrate, plant and fungal lipoxygenases | http://www.dkfz-heidelberg.de/spec/lox-db/ |
| LPFC | Library of protein family core structures | http://www-smi.stanford.edu/projects/helix/LPFC |
| LumbriBASE | ESTs of the earthworm Lumbricus rubellus | http://www.earthworms.org/ |
| MACiE | Mechanism, annotation and classification in enzymes: enzyme reaction mechanisms | http://www-mitchell.ch.cam.ac.uk/macie/ |
| MAGEST | Ascidian (Halocynthia roretzi) gene expression patterns | http://www.genome.ad.jp/magest |
| MAMEP | Molecular anatomy of the mouse embryo project: Gene expression data on mouse embryos | http://mamep.molgen.mpg.de/ |
| Map Viewer | Display of genomic information by chromosomal position | http://www.ncbi.nlm.nih.gov/mapview/ |
| MAPPER | Putative transcription factor binding sites in various genomes | http://bio.chip.org/mapper |
| MBGD | Microbial genome database for comparative analysis | http://mbgd.genome.ad.jp/ |
| MeGX | Marine ecological genomix: genomics and metagenomics of marine bacteria | http://www.Megx.net |
| MEPD | Medaka (freshwater fish Oryzias latipes) gene expression pattern database | http://www.embl.de/mepd/ |
| MeRNA | Metal ion binding sites in RNA | http://merna.lbl.gov |
| MEROPS | Database of proteolytic enzymes (peptidases) | http://merops.sanger.ac.uk/ |
| MetaCyc | Metabolic pathways and enzymes from various organisms | http://metacyc.org |
| MetaGrowth | Growth requirements of bacterial pathogens | http://igs-server.cnrs-mrs.fr/axenic/ |
| Metalloprotein Site | Metal-binding sites in metalloproteins | http://metallo.scripps.edu/ |
| MetaRouter | Compounds and pathways related to bioremediation | http://pdg.cnb.uam.es/MetaRouter |
| MethDB | DNA methylation data, patterns and profiles | http://www.methdb.de/ |
| MFunGD | MIPS mouse functional genomics database | http://mips.gsf.de/genre/proj/mfungd |
| MGC | Mammalian genome collection: Full-length ORFs for human, mouse, and rat genes | http://mgc.nci.nih.gov/ |
| MICdb | Prokaryotic microsatellites | http://www.cdfd.org.in/micas |
| microRNA Registry | Database of microRNAs (small noncoding RNAs) | http://www.sanger.ac.uk/Software/Rfam/mirna/ |
| MIPS | Protein databases at Munich Information Center for Protein Sequences | http://mips.gsf.de/ |
| miRNAMap | microRNA precursors and their mapping to targets in vertebrate genomes | http://mirnamap.mbc.nctu.edu.tw |
| MMDB | NCBI’s database of 3D structures, part of NCBI Entrez | http://www.ncbi.nlm.nih.gov/Structure |
| MNCDB | MIPS Neurospora crassa database | http://mips.gsf.de/proj/neurospora/ |
| Mobile group II introns | A database of group II introns, self-splicing catalytic RNAs | http://www.fp.ucalgary.ca/group2introns/ |
| ModBase | Annotated comparative protein structure models | http://salilab.org/modbase |
| MODOMICS | A database of RNA modification pathways | http://genesilico.pl/modomics/ |
| MolliGen | Genomic data on mollicutes | http://cbi.labri.fr/outils/molligen/ |
| MolMovDB | Database of macromolecular movements: Descriptions of protein and macromolecular motions, including movies | http://bioinfo.mbb.yale.edu/MolMovDB/ |
| Monosaccharide Browser | Space-filling Fischer projections of monosaccharides | http://www.beechtreecommon.org/biochemistry/monosaccharide/ |
| Mouse Genome Informatics | Formerly mouse genome database | http://www.informatics.jax.org/ |
| Mouse SAGE | SAGE libraries from various mouse tissues and cell lines | http://mouse.biomed.cas.cz/sage |
| Mpact | Yeast protein-protein interaction data | http://mips.gsf.de/genre/proj/mpact |
| MPDB | Synthetic oligonucleotides useful as primers or probes | http://www.biotech.ist.unige.it/interlab/mpdb.html |
| MPromDB | Mammalian promoter database | http://bioinformatics.med.ohio-state.edu/MPromDb |
| MTB | Mouse tumor biology database: Tumor types, genes, classification, incidence, pathology | http://tumor.informatics.jax.org/ |
| MtbRegList | Mycobacterium tuberculosis gene regulation | http://www.USherbrooke.ca/vers/MtbRegList |
| MTID | Mouse transposon insertion database | http://mouse.ccgb.umn.edu/transposon/ |
| MulPSSM | Multiple PSSMs of structural and sequence families | http://hodgkin.mbu.iisc.ernet.in/~mulpssm |
| NASCarrays | Nottingham Arabidopsis Stock Centre microarray database | http://affymetrix.arabidopsis.info |
| NCBI Protein database | All protein sequences: translated from GenBank and imported from other protein databases | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein |
| NCBI RefSeq | Non-redundant collection of naturally-occurring biological molecules | http://www.ncbi.nlm.nih.gov/RefSeq/ |
| NCBI Taxonomy | Names of all organisms represented in GenBank | http://www.ncbi.nlm.nih.gov/Taxonomy/ |
| NCBI Viral Genomes | Viral genome resource at NCBI | http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html |
| NCIR | Non-canonical interactions in RNA structures | http://prion.bchs.uh.edu/bp_type/ |
| NCL Mutation Database | Polymorphisms in neuronal ceroid lipofuscinoses genes | http://www.ucl.ac.uk/ncl/ |
| ncRNAs Database | Non-coding RNAs with regulatory functions | http://biobases.ibch.poznan.pl/ncRNA/ |
| NDB | Nucleic acid-containing structures | http://ndbserver.rutgers.edu/ |
| NegProt | Negative Proteome: A tool for comparison of complete proteomes | http://superfly.ucsd.edu/negprot |
| Nematode.net | Parasitic nematode sequencing project | http://nematode.net/ |
| NEMBASE | Nematode sequence and functional data database | http://www.nematodes.org/ |
| NESbase | Nuclear export signals database | http://www.cbs.dtu.dk/databases/NESbase |
| NetAffx | Public Affymetrix probesets and annotations | http://www.affymetrix.com/ |
| NLSdb | Nuclear localization signals | http://cubic.bioc.columbia.edu/db/NLSdb/ |
| NMPdb | Nuclear matrix associated proteins database | http://www.rostlab.org/db/NMPdb/ |
| NONCODE | A database of noncoding RNAs | http://www.bioinfo.org.cn/NONCODE/index.htm |
| NOPdb | Nucleolar proteome database | http://www.lamondlab.com/NOPdb/ |
| NPD | Nuclear protein database | http://npd.hgu.mrc.ac.uk/ |
| NPInter | Noncoding RNA-protein interactions | http://www.bioinfo.org.cn/NPInter |
| NPRD | Nucleosome positioning region database | http://srs6.bionet.nsc.ru/srs6/ |
| NRSub | Non-redundant Bacillus subtilis database at U. Lyon | http://pbil.univ-lyon1.fr/nrsub/nrsub.html |
| NTDB | Thermodynamic data for nucleic acids | http://ntdb.chem.cuhk.edu.hk/ |
| Nuclear Receptor Resource | Nuclear receptor superfamily | http://nrr.georgetown.edu/NRR/nrrhome.htm |
| NucleaRDB | Nuclear receptor superfamily | http://www.receptors.org/NR/ |
| NUREBASE | Nuclear hormone receptors database | http://www.ens-lyon.fr/LBMC/laudet/nurebase.html |
| NURSA | Nuclear receptor signaling atlas | http://www.nursa.org |
| ODB | Operon database | http://odb.kuicr.kyoto-u.ac.jp/ |
| OGD | Oomycete Genomics Database: ESTs and annotation | http://www.oomycete.net/ |
| O-GlycBase | O- and C-linked glycosylation sites in proteins | http://www.cbs.dtu.dk/databases/OGLYCBASE/ |
| Olfactory Receptor Database | Sequences for olfactory receptor-like molecules | http://senselab.med.yale.edu/senselab/ordb/ |
| OMIA | Online Mendelian inheritance in animals: A catalog of animal genetic and genomic disorders | http://www.angis.org.au/omia |
| OMIM | Online Mendelian inheritance in man: A catalog of human genetic and genomic disorders | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM |
| OncoMine | Cancer microarray data by gene or cancer type | http://www.oncomine.org/ |
| ooTFD | Object-oriented transcription factors database | http://www.ifti.org/ootfd |
| Open Proteomics Database | Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium | http://bioinformatics.icmb.utexas.edu/OPD/ |
| OPHID | Online predicted human interaction database | http://ophid.utoronto.ca |
| Oral Cancer Gene Database | Cellular and molecular data for genes involved in oral cancer | http://www.tumor-gene.org/Oral/index.html |
| ORFanage | Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes | http://www.cs.bgu.ac.il/~nomsiew/ORFans |
| ORFDB | Collection of ORFs that are sold by Invitrogen | http://orf.invitrogen.com/ |
| OrthoMCL | Orthologous protein clusters from multiple genomes | http://orthomcl.cbil.upenn.edu |
| Osteo-Promoter Database | Genes in osteogenic proliferation and differentiation | http://www.opd.tau.ac.il |
| PACRAT | Archaeal and bacterial intergenic sequence features | http://www.biosci.ohio-tate.edu/~pacrat |
| PA-GOSUB | Protein sequences from model organisms, GO assignment and subcellular localization | http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html |
| PAHdb | Mutations at the phenylalanine hydroxylase locus | http://www.mcgill.ca/pahdb/ |
| PALI | Phylogeny and alignment of homologous protein structures | http://pauling.mbu.iisc.ernet.in/~pali |
| PANDIT | Protein and associated nucleotide domains with inferred trees | http://www.ebi.ac.uk/goldman-srv/pandit/ |
| PANTHER | Gene products organized by biological function | http://panther.celera.com/ |
| ParaDB | Paralogy mapping in human genomes | http://abi.marseille.inserm.fr/paradb/ |
| PartiGeneDB | Assembled partial genomes for ~250 eukaryotic organisms | http://www.partigenedb.org/ |
| PASS2 | Structural motifs of protein superfamilies | http://ncbs.res.in/~faculty/mini/campass/pass.html |
| PathBase | European mutant mice histopathology database: images | http://www.pathbase.net/ |
| PathDB | Biochemical pathways, compounds and metabolism | http://www.ncgr.org/pathdb |
| Pathguide | A listing of pathway, signal transduction and protein-protein interaction databases | http://pathguide.org |
| PDB | Protein structure databank: all publicly available 3D structures of proteins and nucleic acids | http://www.rcsb.org/pdb |
| PDB_TM | Transmembrane proteins with known 3D structure | http://pdbtm.enzim.hu/ |
| PDB-Ligand | 3D structures of small molecules bound to proteins and nucleic acids | http://www.idrtech.com/PDB-Ligand/ |
| PDB-REPRDB | Representative protein chains, based on PDB entries | http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl |
| PDBrtf | Representation of target families of enzymes in PDB | http://cgl.imim.es/pdbrtf/ |
| PDBSite | 3D structure of protein functional sites | http://srs6.bionet.nsc.ru/srs6/ |
| PDBsum | Summaries and analyses of PDB structures | http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ |
| PDZBase | Protein-protein interactions involving PDZ domains | http://icb.med.cornell.edu/services/pdz/start |
| PEC | Profiling of E. coli chromosome | http://shigen.lab.nig.ac.jp/ecoli/pec |
| PEDANT | Results of an automated analysis of genomic sequences | http://pedant.gsf.de/ |
| PEDB | Prostate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries | http://www.pedb.org/ |
| PEDE | Pig EST data explorer: full-length cDNAs and ESTs | http://pede.gene.staff.or.jp/ |
| PEP | Predictions for entire proteomes: Summarized analyses of protein sequences | http://cubic.bioc.columbia.edu/pep/ |
| PepConfDB | A database of peptide conformations | http://www.peptidome.org/products/list.htm |
| PEPR | Public expression profiling resource: Expression profiles in a variety of diseases and conditions | http://pepr.cnmcresearch.org |
| PepSeeker | Peptide identification and ion information from proteome experiments | http://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl |
| Peptaibol | Peptaibol (antibiotic peptide) sequences | http://www.cryst.bbk.ac.uk/peptaibol/welcome.html |
| PeptideAtlas | Peptides identified in LC-MS/MS proteomics experiments | http://www.peptideatlas.org |
| Pfam | Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains | http://www.sanger.ac.uk/Software/Pfam/ |
| PGDB | Prostate and prostatic diseases gene database | http://www.ucsf.edu/pgdb/ |
| PGTdb | Prokaryotic growth temperature database | http://pgtdb.csie.ncu.edu.tw/ |
| PharmGKB | Pharmacogenomics knowledge base: effect of genetic variation on drug responses | http://www.pharmgkb.org/ |
| PhenomicDB | Comparison of phenotypes of orthologous genes in human and model organisms | http://www.phenomicdb.de/ |
| PHEXdb | PHEX mutations causing X-linked hypophosphatemia | http://www.phexdb.mcgill.ca/ |
| PHI-base | Genes affecting fungal pathogen-host interactions | http://www4.rothamsted.bbsrc.ac.uk/phibase/ |
| Phospho.ELM | S/T/Y protein phosphorylation sites (former PhosphoBase) | http://phospho.elm.eu.org/ |
| Phytophthora Functional Genomics Database | ESTs and expression data from P. infestans and P. sojae | http://www.pfgd.org/pfgd/ |
| PINdb | Proteins interacting in nucleus (human and yeast) | http://pin.mskcc.org/ |
| PINT | Protein-protein interactions thermodynamic database | http://pintdb.dyndns.org/index.html |
| PIR-ALN | Curated database of protein sequence alignments | http://pir.georgetown.edu/pirwww/dbinfo/piraln.html |
| PIR-NREF | PIR’s non-redundant reference protein database | http://pir.georgetown.edu/pirwww/pirnref.shtml |
| PIRSF | Family/superfamily classification of whole proteins | http://pir.georgetown.edu/pirsf/ |
| PKR | Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties | http://pkr.sdsc.edu/html/index.shtml |
| PLACE | Plant cis-acting regulatory DNA elements | http://www.dna.affrc.go.jp/htdocs/PLACE |
| Plant snoRNA DB | snoRNA genes in plant species | http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home |
| PlantCARE | Plant promoters and cis-acting regulatory elements | http://intra.psb.ugent.be:8080/PlantCARE/ |
| PLANTncRNAs | Plant non-coding RNAs | http://www.prl.msu.edu/PLANTncRNAs |
| PlantProm | Plant promoter sequences for RNA polymerase II | http://mendel.cs.rhul.ac.uk/ |
| PlasmoDB | Plasmodium genome database | http://plasmodb.org/ |
| PLPMDB | Pyridoxal-5′-phosphate dependent enzymes mutations | http://www.studiofmp.com/plpmdb/ |
| PMD | Compilation of protein mutant data | http://pmd.ddbj.nig.ac.jp/ |
| PMDB | 3D protein models obtained from structure predictions | http://a.caspur.it/PMDB/ |
| POINT | Prediction of human protein-protein interactome | http://point.nchc.org.tw/ |
| PolyA_DB | A database of mammalian mRNA polyadenylation | http://polya.umdnj.edu/polyadb/ |
| Polymorphix | A database of sequence polymorphisms | http://pbil.univ-lyon1.fr/polymorphix/query.php |
| Poxvirus.org | Poxvirus genomic sequences and gene annotation | http://www.poxvirus.org/ |
| PPD | Protein pKa database | http://www.jenner.ac.uk/ppd/ |
| PPNEMA | Plant-parasitic nematode rRNAs | http://bighost.area.ba.cnr.it/PPNEMA/ |
| PRECISE | Predicted and consensus interaction sites in enzymes | http://precise.bu.edu/precisedb/ |
| PRF | Protein research foundation database of peptides: sequences, literature and unnatural amino acids | http://www.prf.or.jp/en |
| PRIDE | Proteomics identification database | http://www.ebi.ac.uk/pride/ |
| PrimerPCR | PCR primers for eukaryotic and prokaryotic genes | http://bioinfo.ebc.ee/PrimerStudio/ |
| PRINTS | Hierarchical gene family fingerprints | http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ |
| probeBase | rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information | http://www.microbial-ecology.net/probebase |
| ProDom | Protein domain families | http://www.toulouse.inra.fr/prodom.html |
| PRODORIC | Prokaryotic database of gene regulation networks | http://prodoric.tu-bs.de/ |
| ProLysED | A database of bacterial protease systems | http://genome.ukm.my/prolyses/ |
| Prolysis | Proteases and natural and synthetic protease inhibitors | http://delphi.phys.univ-tours.fr/Prolysis/ |
| PromEC | E. coli promoters with experimentally-identified transcriptional start sites | http://margalit.huji.ac.il/promec/ |
| PROMISE | Prosthetic centers and metal ions in protein active sites | http://metallo.scripps.edu/PROMISE |
| ProNIT | Thermodynamic data on protein-nucleic acid interactions | http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html |
| PROPHECY | Profiling of phenotypic characteristics in yeast | http://prophecy.lundberg.gu.se/ |
| ProRule | Functional and structural information on PROSITE profiles | http://www.expasy.org/tools/scanprosite |
| PROSITE | Biologically-significant protein patterns and profiles | http://www.expasy.org/prosite |
| Protein Folding Database | Experimental data on protein folding | http://pfd.med.monash.edu.au |
| Protein-protein interfaces | Interacting residues in protein-protein interfaces in PDB | http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html |
| ProTeus | Signature sequences at the protein N- and C-termini | http://www.proteus.cs.huji.ac.il/ |
| ProTherm | Thermodynamic data for wild-type and mutant proteins | http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html |
| ProtoMap | Hierarchical classification of Swiss-Prot proteins | http://protomap.cornell.edu/ |
| ProtoNet | Hierarchical clustering of Swiss-Prot proteins | http://www.protonet.cs.huji.ac.il/ |
| PseudoBase | Database of RNA pseudoknots | http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html |
| PseudoCAP | Pseudomonas aeruginosa genome database and community annotation project | http://www.pseudomonas.com/ |
| PSIbase | Interaction of proteins with known 3D structures | http://psimap.kaist.ac.kr/ |
| PSORTdb | Protein subcellular localization in bacteria | http://db.psort.org/ |
| pSTIING | Protein signalling, transcriptional interactions and inflammation networks gateway | http://pstiing.licr.org/ |
| PTCH1 Mutation Database | Mutations and SNPs found in PTCH1 gene | http://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html |
| PubChem | Structures and biological activities of small organic molecules | http://pubchem.ncbi.nlm.nih.gov/ |
| PubMed | Citations and abstracts of biomedical literature | http://pubmed.gov/ |
| PUMA2 | Metabolic analysis of complete microbial genomes | http://compbio.mcs.anl.gov/puma2 |
| QPPD | Quantitative PCR Primer Database for human and mouse | http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp |
| QTL Matchmaker | Quantitative trait loci mapping in human, mouse and rat | http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp |
| Rat Genome Database | Rat genetic and genomic data | http://rgd.mcw.edu/ |
| RatMap | Rat genome tools and data | http://ratmap.org/ |
| RB1 Gene Mutation DB | Mutations in the human retinoblastoma (RB1) gene | http://www.d-lohmann.de/Rb/ |
| RDP-II | Ribosomal database project | http://rdp.cme.msu.edu |
| Reactome | http://www.reactome.org/ | |
| REBASE | Restriction enzymes and associated methylases | http://rebase.neb.com/rebase/rebase.html |
| RECODE | Genes using programmed translational recoding in their expression | http://recode.genetics.utah.edu/ |
| RefExA | Reference database for human gene expression analysis | http://www.lsbm.org/db/index_e.html |
| REFOLD | Experimental data on protein refolding and purification | http://refold.med.monash.edu.au |
| RegulonDB | Transcriptional regulation and operon organization in E.coli | http://www.cifn.unam.mx/Computational_Genomics/regulondb/ |
| RESID | Pre-, co- and post-translational protein modifications | http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html |
| Rfam | Non-coding RNA families | http://www.sanger.ac.uk/Software/Rfam/ |
| RHdb | Radiation hybrid map data | http://www.ebi.ac.uk/RHdb |
| Ribonuclease P Database | RNase P sequences, alignments and structures | http://www.mbio.ncsu.edu/RNaseP/home.html |
| RIDOM | rRNA-based differentiation of medical microorganisms | http://www.ridom-rdna.de/ |
| RISSC | Ribosomal internal spacer sequence collection | http://ulises.umh.es/RISSC |
| RNA Modification Database | Naturally modified nucleosides in RNA | http://medlib.med.utah.edu/RNAmods/ |
| RNA SSTRAND | RNA secondary structure data and structural motifs | http://www.rnasoft.ca/sstrand/ |
| RNABase | RNA-containing structures from PDB and NDB | http://www.rnabase.org/ |
| RNAdb | Mammalian noncoding RNA database | http://ncrna.bioinformatics.com.au/ |
| RNAi codex | Clones from mouse, human and rat shRNA libraries | http://codex.cshl.org |
| RNAiDB | RNAi phenotypic analysis of C. elegans genes | http://www.rnai.org/ |
| RNRdb | Ribonucleotide reductase database | http://rnrdb.molbio.su.se/ |
| rOGED | Rat ovarian gene expression database | http://app.mc.uky.edu/kolab/rogedendo.aspx |
| ROSPath | http://rospath.ewha.ac.kr/ | |
| RPG | Ribosomal protein gene database | http://ribosome.miyazaki-med.ac.jp/ |
| RRNDB | rRNA operon numbers in various prokaryotes | http://rrndb.cme.msu.edu/ |
| RsGDB | Rhodobacter sphaeroides genome | http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/ |
| rSNP Guide | SNPs in regulatory gene regions | http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ |
| RTCGD | Mouse retroviral tagged cancer gene database | http://rtcgd.ncifcrf.gov/ |
| RTKdb | Receptor tyrosine kinase sequences | http://pbil.univ-lyon1.fr/RTKdb/ |
| RTPrimerDB | Real-time PCR primer and probe sequences | http://medgen.ugent.be/rtprimerdb/ |
| S/MARt dB | Nuclear scaffold/matrix attached regions | http://smartdb.bioinf.med.uni-goettingen.de/ |
| S4 | Structure-based sequence alignments of SCOP superfamilies | http://compbio.mds.qmw.ac.uk/~james/S4.shtml |
| SAGEmap | NCBI’s resource for SAGE data from various organisms | http://www.ncbi.nlm.nih.gov/SAGE |
| SARS-CoV RNA SSS | Predicted secondary structures of SARS coronavirus RNA | http://www.liuweibo.com/sarsdb/ |
| SBASE | Protein domain sequences and tools | http://www.icgeb.org/sbase |
| SCAdb | Spinocerebellar ataxia candidate gene database | http://ymbc.ym.edu.tw/cgi-bin/SCA/list.cgi?display=map |
| SCMD | Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants | http://yeast.gi.k.u-tokyo.ac.jp/ |
| SCOP | Structural classification of proteins | http://scop.mrc-lmb.cam.ac.uk/scop |
| SCOPEC | Mapping of catalytic function to domain structure | http://www.enzome.com/databases/scopec.php |
| SCOPPI | Structural classification of protein-protein interfaces | http://www.scoppi.org |
| SCOR | Structural classification of RNA: RNA motifs by structure, function and tertiary interactions | http://scor.lbl.gov/ |
| Scorpion | Database of scorpion toxins | http://research.i2r.a-star.edu.sg:8080/scorpion/ |
| SCPD | Saccharomyces cerevisiae promoter database | http://rulai.cshl.edu/SCPD/ |
| SDAP | Structural database of allergenic proteins and food allergens | http://fermi.utmb.edu/SDAP |
| SELEX_DB | DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment | http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ |
| SENTRA | Sensory signal transduction proteins | http://compbio.mcs.anl.gov/sentra/ |
| SEVENS | 7-transmembrane helix receptors (G-protein-coupled) | http://sevens.cbrc.jp/ |
| SGCEdb | Structural genomics of C. elegans | http://sgce.cbse.uab.edu/ |
| SGD | Saccharomyces genome database | http://www.yeastgenome.org/ |
| ShiBase | Shigella database | http://www.mgc.ac.cn/ShiBASE/ |
| SIDDBase | Stress-induced DNA duplex destabilization profiles of complete microbial genomes | http://www.genomecenter.ucdavis.edu/benham/siddbase |
| SIEGE | Smoking Induced Epithelial Gene Expression | http://pulm.bumc.bu.edu/siegeDB |
| SilkDB | Silkworm Bombyx mori ESTs, mutants, photographs | http://www.ab.a.u-tokyo.ac.jp/genome/ |
| SilkSatDb | A microsatellite database of the silkworm Bombyx mori | http://210.212.212.7:9999/PHP/SILKSAT/index.php |
| SIMAP | Similarity matrix of proteins: precomputed similarity data | http://mips.gsf.de/services/analysis/simap/ |
| siRNAdb | Functional human siRNA sequences | http://sirna.cgb.ki.se/ |
| SitesBase | Known ligand binding sites in the PDB | http://www.bioinformatics.leeds.ac.uk/sb/ |
| SKY/M-FISH and CGH | Fluorescent images of chromosomes and cytogenetic data | http://www.ncbi.nlm.nih.gov/sky/ |
| Sloop | Classification of protein loops | http://www-cryst.bioc.cam.ac.uk/~sloop/ |
| Small RNA Database | Small RNAs from prokaryotes and eukaryotes | http://condor.bcm.tmc.edu/smallRNA/smallrna.html |
| SMART | Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains | http://smart.embl-heidelberg.de/ |
| snoRNA-LBME-db | Human C/D box and H/ACA modification guide RNAs | http://www-snorna.biotoul.fr/ |
| SNP Consortium database | SNP Consortium data | http://snp.cshl.org/ |
| SNP500Cancer | Re-sequenced SNPs from 102 reference samples | http://snp500cancer.nci.nih.gov |
| SNPeffect | Phenotypic effects of human coding SNPs | http://snpeffect.vub.ac.be/database.php |
| SOURCE | Functional genomics resource for human, mouse and rat | http://source.stanford.edu/ |
| SPD | Secreted protein database | http://spd.cbi.pku.edu.cn |
| SpliceDB | Canonical and non-canonical mammalian splice sites | http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb |
| SpliceInfo | Modes of alternative splicing in human genome | http://spliceinfo.mbc.nctu.edu.tw/ |
| SpliceNest | A tool for visualizing splicing of genes from EST data | http://splicenest.molgen.mpg.de/ |
| SpodoBase | Genomics of the butterfly Spodoptera frugiperda | http://bioweb.ensam.inra.fr/spodobase/ |
| SRPDB | Signal recognition particle database | http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html |
| SRPDB | Proteins of the signal recognition particles | http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html |
| SSU rRNA Modification Database | Modified nucleosides in small subunit rRNA | http://medstat.med.utah.edu/SSUmods/ |
| STACK | Sequence tag alignment and consensus knowledgebase | http://www.sanbi.ac.za/Dbases.html |
| Stanford Microarray Database | Raw and normalized data from microarray experiments | http://genome-www.stanford.edu/microarray |
| STCDB | http://bibiserv.techfak.uni-bielefeld.de/stcdb/ | |
| StellaBase | Nematostella vectensis (sea anemone) genome | http://stellabase.org. |
| STING report | Amino acid properties in proteins of known structure | http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/ |
| STRBase | Short tandem DNA repeats database | http://www.cstl.nist.gov/div831/strbase/ |
| STRING | Predicted functional associations between proteins | http://string.embl.de/ |
| Structure Superposition Database | Pairwise superposition of TIM-barrel structures | http://ssd.rbvi.ucsf.edu/ |
| SubtiList | Bacillus subtilis genome database at Institut Pasteur | http://genolist.pasteur.fr/SubtiList/ |
| Subviral RNA Database | Viroids and viroid-like RNAs | http://subviral.med.uottawa.ca/ |
| SuperDrug | 2D and 3D chemical structures of various drugs | http://bioinformatics.charite.de/superdrug |
| SUPERFAMILY | Assignments of proteins to structural superfamilies | http://supfam.org/ |
| SuperNatural | Natural compounds and their suppliers | http://bioinformatics.charite.de/supernatural |
| SUPFAM | Grouping of sequence families into superfamilies | http://pauling.mbu.iisc.ernet.in/~supfam |
| SURFACE | Surface residues and functions annotated, compared and evaluated: a database of protein surface patches | http://cbm.bio.uniroma2.it/surface |
| SV40 Large T-Antigen Mutants | Mutations in SV40 large tumor antigen gene | http://supernova.bio.pitt.edu/pipaslab/ |
| SWEET-DB | Annotated carbohydrate structure and substance information | http://www.dkfz-heidelberg.de/spec2/sweetdb/ |
| SWISS-2DPAGE | Annotated 2D gel electrophoresis database | http://www.expasy.org/ch2d/ |
| SWISS-MODEL Repository | Database of annotated 3D protein structure models | http://swissmodel.expasy.org/repository |
| Swiss-Prot | Now UniProt/SwissProt, part of the UniProt knowledgebase | http://www.expasy.org/sprot |
| SynDB | Synaptic protein database | http://syndb.cbi.pku.edu.cn |
| SYSTERS | Systematic re-searching and clustering of proteins | http://systers.molgen.mpg.de/ |
| T1Dbase | A resource for type 1 diabetes research | http://t1dbase.org/ |
| T4-like genome database | Sequences of T4-like bacteriophages from various sources | http://phage.bioc.tulane.edu/ |
| TAED | The adaptive evolution database: A phylogeny-based tool for comparative genomics | http://www.bioinfo.no/tools/TAED |
| TargetDB | Target data from worldwide structural genomics projects | http://targetdb.pdb.org/ |
| TBestDB | Taxonomically broad EST database: protist ESTs | http://tbestdb.bcm.umontreal.ca/searches/welcome.php |
| TCDB | Transporter protein classification database | http://www.tcdb.org/ |
| TcruziDB | Trypanosoma cruzi genome database | http://tcruzidb.org/ |
| TECRdb | Thermodynamics of enzyme-catalyzed reactions | http://xpdb.nist.gov/enzyme_thermodynamics/ |
| TESS | Transcription element search system | http://www.cbil.upenn.edu/tess |
| TGD | Tetrahymena thermophila genome database | www.ciliate.org |
| The Autism Chromosome Rearrangement Database | Curated collection of genomic features related to autism | http://projects.tcag.ca/autism |
| The Chromosome 7 Annotation Project | Human chromosome 7 sequence and annotation | http://www.chr7.org/ |
| The Lafora Database | Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy | http://projects.tcag.ca/lafora/ |
| THGS | Transmembrane helices in genome sequences | http://pranag.physics.iisc.ernet.in/thgs/ |
| TIGR Comprehensive Microbial Resource | Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins | http://www.tigr.org/CMR |
| TIGR Gene Indices | Organism-specific databases of EST and gene sequences | http://www.tigr.org/tdb/tgi.shtml |
| TIGR Gene Indices | Organism-specific databases of EST and gene sequences | http://www.tigr.org/tdb/tgi.shtml |
| TIGR Microbial Database | Lists of completed and ongoing genome projects with links to complete genome sequences | http://www.tigr.org/tdb/mdb/mdbcomplete.html |
| TIGRFAMs | TIGR protein families adapted for functional annotation | http://www.tigr.org/TIGRFAMs |
| TiProD | Tissue-specific promoter database | http://tiprod.cbi.pku.edu.cn:8080/index.html |
| TmaDB | Tissue microarray database | http://www.bioinformatics.leeds.ac.uk/tmadb/ |
| TMPDB | Experimentally-characterized transmembrane topologies | http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/ |
| tmRDB | tmRNA database | http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html |
| tmRNA Website | tmRNA sequences and alignments | http://www.indiana.edu/~tmrna |
| Tooth Development Database | Gene expression in dental tissue | http://bite-it.helsinki.fi/ |
| TopoSNP | Topographic database of non-synonymous SNPs | http://gila.bioengr.uic.edu/snp/toposnp |
| TOPS | Topology of protein structures database | http://www.tops.leeds.ac.uk |
| ToxoDB | Toxoplasma gondii genome database | http://toxodb.org/ |
| TPMD | Taiwan polymorphic microsatellite marker database | http://tpmd.nhri.org.tw/ |
| TRACTOR db | Transcription factors in gamma-proteobacteria database | http://www.tractor.lncc.br/ |
| TRANSCompel® | Composite regulatory elements affecting gene transcription in eukaryotes | http://www.gene-regulation.com/pub/databases.html#transcompel |
| TRANSFAC® | Transcription factors and binding sites | http://transfac.gbf.de/TRANSFAC/index.html |
| TRANSPATH | http://www.biobase.de/pages/products/databases.html | |
| TransportDB | Predicted membrane transporters in complete genomes, classified according to the TC classification system | http://www.membranetransport.org/ |
| Transterm | Codon usage, start and stop signals | http://guinevere.otago.ac.nz/transterm.html |
| TRBase | Tandem repeats in the human genome | http://bioinfo.ex.ac.uk/trbase |
| TRED | Transcriptional regulatory element database | http://rulai.cshl.edu/tred |
| Tree of Life | Information on phylogeny and biodiversity | http://phylogeny.arizona.edu/tree/phylogeny.html |
| TreeBase | Phylogenetic trees and the data matrices used to generate them | http://www.treebase.org/ |
| TreeFam | Tree families database: phylogenetic trees of animal genes | http://www.treefam.org |
| T-REGs | A list of TGFbeta-responsive genes | http://actin.ucd.ie/tgfbeta |
| TrEMBL | Now UniProt/TrEMBL, part of the UniProt knowledgebase | http://www.expasy.org/sprot |
| TRIPLES | Transposon-insertion phenotypes, localization, and expression in Saccharomyces | http://ygac.med.yale.edu/triples/ |
| tRNA sequences | tRNA viewer and sequence editor | http://www.uni-bayreuth.de/departments/biochemie/trna/ |
| trome, trEST and trGEN: | Databases of predicted human protein sequences | ftp://ftp.isrec.isb-sib.ch/pub/databases/ |
| TRRD | Transcription regulatory regions of eukaryotic genes | http://www.bionet.nsc.ru/trrd/ |
| TrSDB | Transcription factor database | http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl |
| TTD | Therapeutic target database | http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp |
| Tumor Gene Family Databases | Cellular, molecular and biological data about genes involved in various cancers | http://www.tumor-gene.org/tgdf.html |
| UCSC Archaeal Genome Browser | Pyrococcus furiosus genome browser | http://archaea.ucsc.edu/ |
| UCSC Genome Browser | Genome assemblies and annotation | http://genome.ucsc.edu/ |
| U-genome | Genome organization in unicellular eukaryotes | http://sege.ntu.edu.sg/wester/ugenome/ |
| UM-BBD | University of Minnesota biocatalysis and biodegradation database | http://umbbd.ahc.umn.edu/ |
| UMLS | Unified medical language system | http://umlsks.nlm.nih.gov/ |
| UniGene | Non-redundant set of eukaryotic gene-oriented clusters | http://www.ncbi.nlm.nih.gov/UniGene/ |
| UniGene | Unified clusters of ESTs and full-length mRNA sequences | http://www.ncbi.nlm.nih.gov/UniGene/ |
| UniParc | UniProt archive, a repository of all protein sequences | http://www.uniprot.org/database/archive.shtml |
| UniProt | Universal protein knowledgebase | http://www.uniprot.org/ |
| UniRef | Clustered sets of related sequences from UniProt | http://www.uniprot.org/database/nref.shtml |
| UniSTS | Unified view of sequence tagged sites with mapping data | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists |
| UniVec | Vector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination | http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html |
| UTRdb/UTRsite | 5′- and 3′-UTRs of eukaryotic mRNAs | http://bighost.area.ba.cnr.it/BIG/UTRHome/ |
| VectorDB | Characterization and classification of nucleic acid vectors | http://genome-www2.stanford.edu/vectordb/ |
| VEGA | Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences | http://vega.sanger.ac.uk/ |
| VIDA | Homologous viral protein families database | http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html |
| VIPERdb | Virus particle explorer: Virus capsid structures | http://viperdb.scripps.edu/ |
| Viral Bioinformatics Resource Center | Virus orthologous genes, gene families and genomes | http://www.virology.ca/ |
| VirFact | Bacterial virulence factors and pathogenicity islands | http://virfact.burnham.org/ |
| VirOligo | Virus-specific oligonucleotides for PCR and hybridization | http://viroligo.okstate.edu/ |
| Virulence Factors | Reference database for microbial virulence factors | http://zdsys.chgb.org.cn/VFs/main.htm |
| VKCDB | Voltage-gated potassium channel database | http://vkcdb.biology.ualberta.ca/ |
| VMD | Virginia Bioinformatics Institute microbial database | http://phytophthora.vbi.vt.edu |
| WILMA | C. elegans annotation database | http://www.came.sbg.ac.at/wilma/ |
| Wnt Database | Wnt proteins and phenotypes | http://www.stanford.edu/~rnusse/wntwindow.html |
| WorfDB | C. elegans ORFeome | http://worfdb.dfci.harvard.edu/ |
| WormBase | Data repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways | http://www.wormbase.org/ |
| Xpro | Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes | http://origin.bic.nus.edu.sg/xpro/ |
| YDPM | Yeast deletion project and mitochondria database | http://www-deletion.stanford.edu/YDPM/YDPM_index.html |
| Yeast Intron Database | Ares lab database of splicesomal introns in S. cerevisiae | http://www.cse.ucsc.edu/research/compbio/yeast_ introns.html |
| Yeast snoRNA Database | Yeast small nucleolar RNAs | http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html |
| YEASTRACT | Yeast search for transcriptional regulators and consensus tracking | http://www.yeastract.com |
| YGOB | Yeast gene order browser | http://wolfe.gen.tcd.ie/ygob |
| yMGV | Yeast microarray global viewer | http://www.transcriptome.ens.fr/ymgv/ |
| YRC PDR | Yeast resource center public data repository | http://www.yeastrc.org/pdr/ |
| ZFIN | Zebrafish information network | http://zfin.org/ |