List of Genetic Labs

Labs that are regularly Publishing gene maps:

RNA SequencesSubviral RNA databasehttp://132.210.163.235/subviral/home.cgiDatabase of viroids and viroid-like RNAs
CADBhttp://144.16.71.148Conformation angles of protein structures, with associated crystallographic data
Comparative
Genomics
ParaDBhttp://abi.marseille.inserm.fr/paradbParalogy mapping in human genomes
ALFREDhttp://alfred.med.yale.edu/Allele frequencies and DNA polymorphisms
DPInteracthttp://arep.med.harvard.edu/dpinteract/Binding sites for E. coli DNA-binding proteins
ASTRALhttp://astral.stanford.edu/Sequences of domains of known structure, selected subsets, and sequence-structure correspondences
PathologyFIMMhttp://baygenomics.ucsf.eduIdentification of genes relevant to cardiovascular and pulmonary disease
HyPaLibhttp://bibiserv.techfak.Structural elements characteristic for classes of RNA
MitoDromehttp://bighost.area.ba.cnr.it/BIG/MitoDromeDrosophila nuclear genes encoding proteins targeted to the mitochondrion
Genomic

Databases
AMmtDBhttp://bighost.area.ba.cnr.it/mitochondriomeMetazoan mitochondrial genes
PLMItRNAhttp://bighost.area.ba.cnr.it/PLMItRNA/Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
Genomic

Databases
MitoNuc/MitoAlnhttp://bighost.area.ba.cnr.it/srs/Nuclear genes coding for mitochondrial proteins
RNA SequencesUTRdb/UTRsitehttp://bighost.area.ba.cnr.it/srs6/5′ and 3′ UTRs of eukaryotic mRNAs and relevant functional patterns
Biomolecular Interaction Network Database (BIND)http://binddb.orgMolecular interactions, complexes, and pathways
SRPDBhttp://bio.lundberg.gu.se/dbs/Structural and functional information on signalrecognition particles
RNA Sequences5S Ribosomal RNA Databasehttp://biobases.ibch.poznan.pl/5SData5S rRNA sequences
RNA SequencesNoncoding regulatory RNAs Databasehttp://biobases.ibch.poznan.pl/ncRNANoncoding RNAs with regulatory functions
RNA SequencesCollection of mRNA-like Noncoding RNAshttp://biobases.ibch.poznan.pl/ncRNA/Non-protein-coding RNA transcripts
Plant snoRNA DBhttp://bioinf.scri.sari.ac.uk/snoRNA genes in plant species
Mutation

Databases
BTKbasehttp://bioinf.uta.fi/BTKbase/Mutation registry for X-linked agammaglobulinemia
Mutation

Databases
KinMutBasehttp://bioinf.uta.fi/KinMutBase/Disease-causing protein kinase mutations
Database of Macromolecular Movementshttp://bioinfo.mbb.yale.edu/MolMovDB/Descriptions of protein and macromolecular motions, including movies
Gene Identification and StructurePromEChttp://bioinfo.md.huji.ac.il/marg/promecE. coli mRNA promoters with experimentally identified transcriptional start sites
Protein Sequence MotifsTMPDBhttp://bioinfo.si.hirosaki-u.ac.jp/~TMPDBExperimentally-characterized transmembrane topologies
Genomic

Databases
GeneCardshttp://bioinfo.weizmann.ac.il/cardsIntegrated database of human genes, maps, proteins and diseases
Genomic

Databases
CroW 21http://bioinfo.weizmann.ac.il/crow21/Human chromosome 21 database
Protein

Databases
HORDEhttp://bioinfo.weizmann.ac.il/HORDE/Catalog of human genetic and genomic disorders
Guide RNA Databasehttp://biosun.bio.tu-darmstadt.de/Guide RNA sequences
Protein

Databases
ESTHERhttp://bioweb.ensam.inra.fr/ESTHER/Esterases and alpha/beta hydrolase enzymes and relatives
Tooth Development Databasehttp://bite-it.helsinki.fi/Gene expression in dental tissue
Protein Sequence MotifsBLOCKShttp://blocks.fhcrc.org/Conserved sequence regions of protein families
Genomic

Databases
EcoGenehttp://bmb.med.miami.edu/EcoGene/EcoWeb/E. coli K-12 sequences
Gene

Expression
BodyMaphttp://bodymap.ims.u-tokyo.ac.jp/Human and mouse gene expression data
Cytokine Gene Polymorphism in Human Diseasehttp://bris.ac.uk/pathandmicro/Cytokine gene polymorphism literature database
Genomic

Databases
BSDhttp://bsd.cme.msu.eduComparative data on known biodegradative organisms
Gene

Expression
ASDBhttp://cbcg.nersc.gov/asdbProtein products and expression patterns of alternatively-spliced genes
CKAAPs DBhttp://ckaap.sdsc.eduStructurally-similar proteins with dissimilar sequences
CEhttp://cl.sdsc.edu/ce.htmlCombinatorial Extension: A Resource to Compute and Review 3-D Protein Structure Alignments
Genomic

Databases
CnidBasehttp://cnidbase.bu.edu/Cnidarian evolutionary genomics and gene expression
Mutation

Databases
SV40 Large T-Antigen Mutant Databasehttp://colon.bio.pitt.edu:5243/SV40/index.htmlMutations in SV40 large tumor antigen gene
Gene Identification and StructureCOMPELhttp://compel.bionet.nsc.ru/Database on composite regulatory elements affecting gene transcription in eukaryotes
Mutation

Databases
Asthma Gene Databasehttp://cooke.gsf.de/asthmagen/main.cfmLinkage and mutation studies on the genetics of asthma and allergy
Comparative

Genomics
CORGhttp://corg.molgen.mpg.deConserved non-coding sequence blocks
Protein Sequence MotifsASC-Active Sequence Collectionhttp://crisceb.unina2.it/ASC/Biologically-active short amino acid sequences
Protein Sequence MotifsNLSdbhttp://cubic.bioc.columbia.edu/db/NLSdbNuclear localization signals
Proteome

Resources
PEP: Predictions for Entire Proteomeshttp://cubic.bioc.columbia.edu/pep/Signalling domain sequences
Decoys ‘R’ Ushttp://dd.stanford.edu/Computer-generated protein conformations based on sequence data
Protein

Databases
Prolysishttp://delphi.phys.univ-tours.fr/Prolysis/Proteases and natural and synthetic protease inhibitors
DIPhttp://dip.doe-mbi.ucla.edu/Catalog of protein-protein interactions
Metabolic Pathways and Cellular RegulationMetaCychttp://ecocyc.orgMetabolic pathways and enzymes from various organisms
Metabolic Pathways and Cellular RegulationEcoCychttp://ecocyc.org/E. coli K-12 genome, gene products, and metabolic pathways
Gene Identification and StructureDBTBShttp://elmo.ims.u-tokyo.ac.jp/dbtbs/Bacillus subtilis promoters and transcription factors
Genomic

Databases
ERGOhttp://ergo.integratedgenomics.com/ERGOIntegrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature
FAMSBASEhttp://famsbase.bio.nagoya-u.ac.jp/Protein three-dimensional structural models
Protein

Databases
SDAPhttp://fermi.utmb.edu/SDAPSequences, structures and IgE epitopes of allergenic proteins
PathologyINFEVERShttp://fmf.igh.cnrs.fr/infeversFamilial Mediterranean Fever and hereditary inflammatory disorder mutation data
PathologyMetaFMFhttp://fmf.igh.cnrs.fr/metaFMF/index_us.htmlFamilial Mediterranean Fever phenotype-genotype correlation
Genomic

Databases
Full-Malariahttp://fullmal.ims.u-tokyo.ac.jpFull-length cDNA library from erythrocytic-stage Plasmodium falciparum
Proteome

Resources
GELBANKhttp://gelbank.anl.gov2D-gel electrophoresis patterns from completed genomes
Genetic and Physical MapsGeneLochttp://genecards.weizmann.ac.il/udb/Integrated human maps
Gene

Expression
Mouse Atlas and Gene Expression Databasehttp://genex.hgu.mrc.ac.ukSpatially-mapped gene expression data
SubtiListhttp://genolist.pasteur.fr/SubtiListBacillus subtilis genome
Protein

Databases
Histone Databasehttp://genome.nhgri.nih.gov/histones/Histone and histone fold sequences and structures
Protein

Databases
Homeodomain Resourcehttp://genome.nhgri.nih.gov/homeodomainHomeodomain sequences, structures, and related genetic and genomic information
Non-redundant, gene-oriented clusters:UCSC Genome Browserhttp://genome.ucsc.edu/Genome assemblies and annotation
Gene

Expression
Stanford Microarray Databasehttp://genome-www.stanford.edu/microarrayRaw and normalized data from microarray experiments
Saccharomyces Genome Database (SGD)http://genome-www.stanford.edu/SaccharomycesSaccharomyces cerevisiae genome
Genetic and Physical MapsGenMapDBhttp://genomics.med.upenn.edu/genmapdbMapped human BAC clones
GénoPlante-Infohttp://genoplante-info.infobiogen.frPlant genomic data derived from the Génoplante consortium
FLAGdb/FSThttp://genoplante-info.infobiogen.frArabidopsis thaliana T-DNA transformants
Protein

Databases
GenProtEChttp://genprotec.mbl.eduEscherichia coli K-12 genome, gene products, and homologs
PathologyGOLD.dbhttp://gold.tugraz.atGenes, proteins, and pathways implicated in lipid-associated disorders
Kidney Development Databasehttp://golgi.ana.ed.ac.uk/kidhome.htmlKidney development and gene expression
Gene Identification and StructureGene Resource Locatorhttp://grl.gi.u-tokyo.ac.jpAlignment of ESTs with finished human sequence
ModBasehttp://guitar.rockefeller.edu/modbaseAnnotated comparative protein structure models
Mutation

Databases
HGVbasehttp://hgvbase.cgb.ki.se/Human Genome Variation database
Protein

Databases
trEST, trGEN and Hitshttp://hits.isb-sib.chPredicted protein sequences
Protein DatabasesHIV RT and Protease Sequence Databasehttp://hivdb.stanford.eduHIV reverse transcriptase and protease sequences
Mutation DatabasesHIV-RThttp://hivdb.stanford.edu/hiv/HIV reverse transcriptase and protease sequence variation
HIV Sequence Databasehttp://hiv-web.lanl.gov/HIV RNA sequences
Protein DatabasesHIV Molecular Immunology Databasehttp://hiv-web.lanl.gov/immunology/HIV epitopes
Protein DatabasesHomeobox Pagehttp://homeobox.biosci.ki.seInformation relevant to homeobox proteins, classification, and evolution
Comparative GenomicsHomophilahttp://homophila.sdsc.eduRelationship of human disease genes to genes in Drosophila
HugeIndexhttp://hugeindex.orgmRNA expression levels of human genes in normal tissues
IRESdbhttp://ifr31w3.toulouse.inserm.fr/Internal ribosome entry sites
Genomic DatabasesGOLDhttp://igweb.integratedgenomics.com/GOLD/Information regarding complete and ongoing genome projects
Protein DatabasesIMGThttp://imgt.cines.fr:8104/Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
Kabat Databasehttp://immuno.bme.nwu.edu/Sequences of proteins of immunological interest
Mutation DatabasesMutation Spectra Databasehttp://info.med.yale.edu/mutbase/Mutations in viral, bacterial, yeast, and mammalian genes
InterDomhttp://InterDom.lit.org.sgPutative protein domain interactions
Gene Identification and StructureExInthttp://intron.bic.nus.edu.sg/exint/exint.htmlExon-intron structure of eukaryotic genes
Protein DatabasesABCdbhttp://ir2lcb.cnrs-mrs.fr/ABCdb/ABC transporters
Genetic and Physical MapsIXDBhttp://ixdb.mpimg-berlin-dahlem.mpg.dePhysical maps of human chromosome X
Vectordbhttp://life.nthu.edu.tw/Characterization and classification of nucleic acid vectors
WILMAhttp://lore.came.sbg.ac.at:8080/Caenorhabditis elegans annotation
DAtAhttp://luggagefast.Stanford.EDU/Annotated coding sequences from Arabidopsis
RNA SequencesSmall RNA Databasehttp://mbcr.bcm.tmc.edu/smallRNADirect sequencing of small RNA sequences from prokaryotes and eukaryotes
Comparative GenomicsMBGDhttp://mbgd.genome.ad.jpMicrobial genome database for comparative genomic analysis
Gene Identification and StructureEIDhttp://mcb.harvard.edu/gilbert/EID/Protein-coding, intron-containing genes
MEPDhttp://medaka.dsp.jst.go.jp/MEPDGene expression data from the small freshwater fish Medaka
RNA SequencesRNA Modification Databasehttp://medlib.med.utah.edu/RNAmods/Naturally modified nucleosides in RNA
GOBASEhttp://megasun.bch.umontreal.ca/Organelle genome database
Gene Identification and StructurePlantPromhttp://mendel.cs.rhul.ac.uk/Proximal promoter sequences for RNA polymerase II
MetaFamhttp://metafam.ahc.umn.edu/Integrated protein family information
Mutation Databasesp53 Databaseshttp://metalab.unc.edu/dnam/mainpage.htmlMutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Metalloprotein Database and Browserhttp://metallo.scripps.edu/Metal-binding sites in metalloproteins
Protein DatabasesPROMISEhttp://metallo.scripps.edu/PROMISE/Prosthetic centers and metal ions in protein active sites
MPIMPhttp://millar3.biochem.uwa.edu.au/Mitochondrial protein import machinery of plants
Genomic DatabasesMITOPhttp://mips.gsf.de/proj/medgen/mitop/Mitochondrial proteins, genes, and diseases
Genomic DatabasesMOsDBhttp://mips.gsf.de/proj/riceOryza sativa genome
Gene Identification and StructureSputnikhttp://mips.gsf.de/proj/sputnikFunctional annotation of clustered plant ESTs
RsGDBhttp://mmg.uth.tmc.edu/sphaeroidesRhodobacter sphaeroides genome
MolMovDBhttp://MolMovDB.orgDatabase of macromolecular movements
Protein Sequence MotifseMOTIFhttp://motif.stanford.edu/emotifProtein sequence motif determination and searches
Gene ExpressionMTIDhttp://mouse.ccgb.umn.edu/transposon/Sleeping beauty transposon insertion in mice
PASS2http://ncbs.res.in/%7Efaculty/Structural motifs of protein superfamilies
NDBhttp://ndbserver.rutgers.edu/Nucleic acid-containing structures
Protein DatabasesNuclear Protein Database (NPD)http://npd.hgu.mrc.ac.ukProteins localized in the nucleus
Nuclear Receptor Resourcehttp://nrr.georgetown.edu/nrr/nrr.htmlNuclear receptor superfamily
NTDBhttp://ntdb.chem.cuhk.edu.hkThermodynamic data for nucleic acids
Gene Identification and StructureIDB/IEDBhttp://nutmeg.bio.indiana.edu/intron/index.htmlIntron sequence and evolution
European Ribosomal RNA Databasehttp://oberon.rug.ac.be:8080/Alignment of ribosomal RNA sequences with secondary structure information
Gene Identification and StructurePlantCAREhttp://oberon.rug.ac.be:8080/PlantCARE/index.htmlPlant transcription sites
PANTHERhttp://panther.celera.comGene products organized by biological function
PALIhttp://pauling.mbu.iisc.ernet.in/~paliPhylogeny and alignment of homologous protein structures
Protein Sequence MotifsSUPFAMhttp://pauling.mbu.iisc.ernet.in/~supfamGrouping of sequence families into superfamilies
Genomic DatabasesEMGlibhttp://pbil.univ-lyon1.fr/emglib/emglib.htmlCompletely sequenced microbial genomes from bacteria, archaea, yeast
Genomic DatabasesNRSubhttp://pbil.univ-lyon1.fr/nrsub/nrsub.htmlBacillus subtilis genome
Protein DatabasesRTKdbhttp://pbil.univ-lyon1.fr/RTKdbReceptor tyrosine kinase sequences
Gene ExpressionFlyViewhttp://pbio07.uni-muenster.de/Drosophila development and genetics
Genomic DatabasesPEDANT genome databasehttp://pedant.gsf.deAutomated analysis of genomic sequences
Protein DatabasesProtein Information Resource (PIR)http://pir.georgetown.eduComprehensive, annotated, non-redundant protein sequence database
ProClasshttp://pir.georgetown.edu/Protein families defined by PIR superfamilies and PROSITE patterns
Protein DatabasesPIR-NREFhttp://pir.georgetown.edu/pirwww/pirnref.shtmlNon-redundant reference database with comprehensive protein sequences
Protein DatabasesPKRhttp://pkr.sdsc.edu/html/index.shtmlProtein kinase sequences, enzymology, genetics, and molecular and structural properties
Protein DatabasesPlantsP/PlantsThttp://plantsp.sdsc.eduFunctional genomics databases focusing on protein involved in plant phosphorylation and membrane transport
PlasmoDBhttp://PlasmoDB.orgThe Plasmodium falciparum Genome Database
Mutation DatabasesPMDhttp://pmd.ddbj.nig.ac.jp/Compilation of protein mutant data
PRESAGEhttp://presage.berkeley.edu/Protein structures with experimental and predictive annotations
RNA SequencesNCIRhttp://prion.bchs.uh.edu/bp_type/Non-standard base-base interactions in known RNA structures
ProDomhttp://prodes.toulouse.inra.fr/prodom/Protein domain families
Metabolic Pathways and Cellular RegulationPRODORIChttp://prodoric.tu-bs.deProkaryotic database of gene regulation and regulatory networks
DSMMhttp://projects.eml.org/mcm/database/dsmmDatabase of simulated molecular motions
Protein Sequence MotifsProtoMaphttp://protomap.cornell.eduAutomated hierarchical classification of SWISS-PROT proteins
SRPDBhttp://psyche.uthct.edu/dbs/Signal recognition particle RNA, SRP protein and SRP receptor sequences and alignments
tmRDBhttp://psyche.uthct.edu/dbs/tmRNA (10Sa RNA) sequences and alignments
RNA SequencesAREDhttp://rc.kfshrc.edu.sa/ared/AU-rich element-containing mRNAs
RNA SequencesRibosomal Database Project (RDP II)http://rdb.cme.msu.edurRNA sequence data, analysis tools, alignments and phylogenies
Proteome ResourcesREBASEhttp://rebase.neb.com/rebase/rebase.htmlRestriction enzymes and associated methylases
Gene ExpressionRECODEhttp://recode.genetics.utah.eduGenes using programmed translational recoding in their expression
Rat Genome Databasehttp://rgd.mcw.eduRat genetic and genomic data
Genomic DatabasesINEhttp://rgp.dna.affrc.go.jp/giot/INE.htmlRice genetic and physical maps and sequence data
Rice GAAShttp://RiceGaas.dna.affrc.go.jp/Rice genome sequence
Protein DatabasesAARSDBhttp://rose.man.poznan.pl/aars/index.htmlAminoacyl-tRNA synthetase sequences
Gene Identification and StructureRRNDBhttp://rrndb.cme.msu.eduVariation in prokaryotic ribosomal RNA operons
SCOPhttp://scop.mrc-lmb.cam.ac.uk/scop/Familial and structural protein relationships
SCORhttp://scor.lbl.govRNA structural relationships
Olfactory Receptor Databasehttp://senselab.med.yale.edu/senselab/Sequences for olfactory receptor-like molecules
SEVENShttp://sevens.cbrc.jp7-transmembrane helix receptors
Protein Sequence MotifsSMARThttp://smart.embl-heidelberg.de/Signalling domain sequences
Gene Identification and StructureSNP Consortium databasehttp://snp.cshl.orgSingle Nucleotide Polymorphisms for biomedical research
SOURCEhttp://source.stanford.eduFunctional genomic resource for annotations ontologies, and expression data
PPMdbhttp://sphinx.rug.ac.be:8080/Arabidopsis plasma membrane protein sequence and expression data
GTOPhttp://spock.genes.nig.ac.jp/Structures of small molecules (hetero-compounds)
PDBsumhttp://srs.ebi.ac.uk/Molecular Probe Database
PSSHhttp://srs3d.ebi.ac.uk/Alignment between protein sequences and tertiary structures
Structure-Superposition Databasehttp://ssd.rbvi.ucsf.eduPairwise superposition of TIM-barrel structures
SUPERFAMILYhttp://supfam.orgAssignments of proteins to structural superfamilies
MHC-Peptide Interaction Databasehttp://surya.bic.nus.edu.sg/mpidClass I and class II MHC-peptide complexes
Protein Sequence MotifsSYSTERShttp://systers.molgen.mpg.de/Classification of protein sequences into disjoint clusters with annotations from various other resources
Transgenic/Targeted Mutation Databasehttp://tbase.jax.org/Information on transgenic animals and targeted mutations
Mutation DatabasesGRAP Mutant Databaseshttp://tinyGRAP.uit.no/GRAP/Mutants of family A G-Protein Coupled Receptors (GRAP)
Tree of Lifehttp://tolweb.org/tree/phylogeny.htmlInformation on phylogeny and biodiversity
Genomic DatabasesToxoDB: The Toxoplasma gondii Genome Databasehttp://ToxoDB.orgApicomplexan parasite Toxoplasma gondii genome
TRANSFAChttp://transfac.gbf.de/TRANSFAC/index.htmlTranscription factors and binding sites
PathologyMouse Tumor Biology Database (MTB)http://tumor.informatics.jax.orgMouse tumor names, classification, incidence, pathology, genetic factors
Genomic DatabasesCropNethttp://ukcrop.net/Genome mapping in crop plants
RNA SequencesRISCChttp://ulises.umh.es/RISSCRibosomal 16S-23S RNA gene spacer regions
Metabolic Pathways and Cellular RegulationThe University of Minnesota Biocatalysis Biodegradation Databasehttp://umbbd.ahc.umn.edu/Curated information on microbial catabolism and related biotransformations
Gene Identification and StructureTransTermhttp://uther.otago.ac.nz/Transterm.htmlCodon usage, start and stop signals
VirOligohttp://viroligo.okstate.eduVirus-specific oligonucleotides for PCR and hybridization
MHCPEPhttp://wehih.wehi.edu.au/mhcpep/MHC-binding peptides
WIT2http://wit.mcs.anl.gov/WIT2/Integrated system for functional curation and development of metabolic models
WorfDBhttp://worf.dfci.harvard.eduCaenorhabditis elegans ORFeome
Gene ExpressionNetAffixhttp://www.affymetrics.comPublic Affymetrix probesets and annotations
Gene Identification and StructureAllGeneshttp://www.allgenes.orgHuman and mouse gene index integrating gene, transcript and protein annotation
Mutation DatabasesOnline Mendelian Inheritance in Animalshttp://www.angis.org.au/omiaCatalog of animal genetic and genomic disorders
The Arabidopsis Information Resource (TAIR)http://www.arabidopsis.orgArabidopsis thaliana genome
Protein DatabasesAraC/XylS databasehttp://www.AraC-XylS.orgAraC/XylS protein family of positive regulators in bacteria
Yeast snoRNA Databasehttp://www.bio.umass.edu/biochem/Yeast small nucleolar RNAs
TRANSPATHhttp://www.biobase.de/pages/Gene regulatory networks and microarray analysis
VIDAhttp://www.biochem.ucl.ac.uk/Virus genome open reading frames
Gene3Dhttp://www.biochem.ucl.ac.uk/bsmPrecalculated structural assignments for genes within whole genomes
VIDAhttp://www.biochem.ucl.ac.uk/bsm/Homologous viral protein families
CATHhttp://www.biochem.ucl.ac.uk/bsm/cath/Hierarchical classification of protein domain structures
PDBsumhttp://www.biochem.ucl.ac.uk/bsm/pdbsumSummaries and analyses of PDB structures
Metabolic Pathways and Cellular RegulationKlothohttp://www.biocheminfo.org/klothoCollection and categorization of biological compounds
BioImagehttp://www.bioimage.orgSearchable database of multidimensional biological images
PRINTShttp://www.bioinf.man.ac.uk/Hierarchical gene family fingerprints
Genomic DatabasesOGRehttp://www.bioinf.man.ac.uk/ogreComplete mitochondrial genome sequences for 200 metazoan species
Gene Identification and StructureASAPhttp://www.bioinformatics.ucla.edu/ASAPAlternative spliced isoforms
Protein DatabasesEndogenous GPCR Listhttp://www.biomedcomp.com/GPCR.htmlG protein-coupled receptors; expression in cell lines
Gene Identification and StructurePACRAThttp://www.biosci.ohio-state.edu/~pacratArchaeal and bacterial intergenic sequence features
MPDBhttp://www.biotech.ist.unige.it/Information on synthetic oligonucleotides proven useful as primers or probes
BioMagResBankhttp://www.bmrb.wisc.edu/NMR spectroscopic data from proteins, peptides, and nucleic acids
STRINGhttp://www.bork.embl-heidelberg.de/STRING/Predicted functional associations between proteins
Cytokine Gene Polymorphism Databasehttp://www.bris.ac.uk/pathandmicro/Cytokine gene polymorphisms, in vitro expression and disease-association studies
Mutation DatabasesCASRDBhttp://www.casrdb.mcgill.ca/Calcium Sensing Receptor Locus Mutation Database
Genomic DatabasesCATMAhttp://www.catma.orgArabidopsis gene sequence tags (GSTs)
expressionEPConDBhttp://www.cbil.upenn.edu/EPConDBEndocrine pancreas consortium database
Metabolic Pathways and Cellular RegulationEpoDBhttp://www.cbil.upenn.edu/EpoDB/Genes expressed during human erythropoiesis
EpoDBhttp://www.cbil.upenn.edu/EpoDB/index.htmlGenes expressed in vertebrate red blood cells
TESShttp://www.cbil.upenn.edu/tessTranscription element search system
PDB-REPRDBhttp://www.cbrc.jp/papia/papia.htmlRepresentative protein chains, based on PDB entries
PhosphoBasehttp://www.cbs.dtu.dk/Protein phosphorylation sites
Protein Sequence MotifsNESbasehttp://www.cbs.dtu.dk/databases/NESbaseNuclear export signals
Protein Sequence MotifsO-GLYCBASEhttp://www.cbs.dtu.dk/databases/OGLYCBASE/Glycoproteins and O-linked glycosylation sites
CSDhttp://www.ccdc.cam.ac.uk/Crystal structure information for organic and metal organic compounds
Gene Identification and StructureMICdbhttp://www.cdfd.org.in/micasProkaryotic microsattelites
Protein DatabasesCSDBasehttp://www.chemie.uni-marburg.de/~csdbaseCold shock domain-containing proteins
RegulonDBhttp://www.cifn.unam.mx/E. coli transcriptional regulation and operon organization
Protein DatabasesFUNPEPhttp://www.cmbi.kun.nl/swift/FUNPEP/library/Low-complexity or compositionally-biased protein sequences
Protein DatabasesEXProthttp://www.cmbi.nl/exprotProteins with experimentally-verified function
Peptaibolhttp://www.cryst.bbk.ac.uk/Peptaibol (antibiotic peptide) sequences
Introneratorhttp://www.cse.ucsc.edu/RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
Ares Lab Intron Sitehttp://www.cse.ucsc.edu/research/Yeast spliceosomal introns
STRBasehttp://www.cstl.nist.gov/div831/strbase/Short tandem DNA repeats
Mutation DatabasesPTCH Mutation Databasehttp://www.cybergene.se/PTCH/ptchbase.htmlMutations and SNPs found in PTCH1
Axeldbhttp://www.dkfz-heidelberg.de/Gene expression in Xenopus
SWEET-DBhttp://www.dkfz-heidelberg.de/Annotated carbohydrate structure and substance information
Mutation DatabasesRB1 Gene Mutation Databasehttp://www.d-lohmann.de/Rb/Mutations in the human retinoblastoma (RB1) gene
Gene Identification and StructurePLACEhttp://www.dna.affrc.go.jp/htdocs/PLACEPlant cis-acting regulatory elements
Genetic and Physical MapsGenAtlashttp://www.dsi.univ-paris5.fr/genatlas/Human genes, markers, and phenotypes
Gene ExpressionArrayExpresshttp://www.ebi.ac.uk.arrayexpressPublic collection of microarray gene expression data
Protein Sequence MotifsCluSTrhttp://www.ebi.ac.uk/clustr/Automatic classification of SWISS-PROT + TrEMBL proteins into related groups
International Nucleotide Sequence Database Collaboration:EMBL Nucleotide Sequence Databasehttp://www.ebi.ac.uk/embl/All known nucleotide and protein sequences
Protein DatabasesIMGT/HLAhttp://www.ebi.ac.uk/imgt/hla/Human major histocompatibility comples
Protein DatabasesIMGT/MHC Databasehttp://www.ebi.ac.uk/imgt/mhcMajor histocompatibility complex sequences
Protein DatabasesInterProhttp://www.ebi.ac.uk/interproProtein families and domains
Protein Sequence MotifsInterProhttp://www.ebi.ac.uk/interpro/Integrated documentation resource for protein families, domains, and sites
E-MSDhttp://www.ebi.ac.uk/msdCollected data on macromolecular structures
Proteome ResourcesProteome Analysis Databasehttp://www.ebi.ac.uk/proteome/Online application of interpro and clustr for the functional classification of proteins in whole genomes
Genetic and Physical MapsRHdbhttp://www.ebi.ac.uk/RHdbRadiation hybrid map data
Non-redundant, gene-oriented clusters:Ensemblhttp://www.ensembl.orgAnnotated information on eukaryotic genomes
NUREBASEhttp://www.ens-lyon.fr/LBMC/Nuclear Receptor dataBase
Gene Identification and StructureEPDhttp://www.epd.isb-sib.ch/Eukaryotic POL II promoters with experimentally-determined transcription start sites
Proteome ResourcesSWISS-2DPAGEhttp://www.expasy.ch/ch2d/Annotated two-dimensional polyacrylamide gel electrophoresis database
Metabolic Pathways and Cellular RegulationENZYMEhttp://www.expasy.ch/enzyme/Enzyme nomenclature
Protein Sequence MotifsPROSITEhttp://www.expasy.ch/prosite/Biologically-significant protein patterns and profiles
Protein DatabasesSWISS-PROT/TrEMBLhttp://www.expasy.ch/sprotCurated protein sequences
16S and 23S Ribosomal RNA Mutation Databasehttp://www.fandm.edu/Departments/16S and 23S rRNA mutations
RNA SequencesDatabase for mobile group II intronshttp://www.fp.ucalgary.ca/group2intronsDatabase for mobile group II introns
Genomic DatabasesFlyBasehttp://www.fruitfly.orgDrosophila sequences and genomic information
Genomic DatabasesHGT-DBhttp://www.fut.es/~debb/HGT/Putative horizontally-transferred genes in prokaryotic genomes
Genetic and Physical MapsGDBhttp://www.gdb.orgHuman genes and genomic maps
Genewhttp://www.gene.ucl.ac.uk./cgi-bin/Approved symbols for all human genes
TRANSCompelhttp://www.gene-regulation.com/pub/Composite regulatory elements
Proteome ResourcesAAindexhttp://www.genome.ad.jp/dbget/Physicochemical properties of peptides
Metabolic Pathways and Cellular RegulationLIGANDhttp://www.genome.ad.jp/dbget/ligand.htmlEnzymatic ligands, substrates, and reactions
Metabolic Pathways and Cellular RegulationKyoto Encyclopedia of Genes and Genomes (KEGG)http://www.genome.ad.jp/kegg/Metabolic and regulatory pathways
MAGESThttp://www.genome.ad.jp/magest/Maboya ( the ascidian, Halocynthia roretzi ) Gene Expression patterns and Sequence Tags
GlycoSuiteDBhttp://www.glycosuite.comN- and O-linked glycan structures and biological source information
Protein DatabasesGPCRDBhttp://www.gpcr.org/7tm/G protein-coupled receptors
GrainGeneshttp://www.graingenes.orgGenomic database for small-grain crops
Protein DatabasesDExH/D Family Databasehttp://www.helicase.net/dexhd/dbhome.htmDEAD-box, DEAH-box, and DExH-box proteins
Mutation DatabasesHuman Gene Mutation Database (HGMD)http://www.hgmd.orgKnown (published) gene lesions underlying human inherited disease
Mutation DatabasesHuman PAX2 Allelic Variant Databasehttp://www.hgu.mrc.ac.uk/Softdata/PAX2/Mutations in human PAX2 gene
Mutation DatabasesHuman PAX6 Allelic Variant Databasehttp://www.hgu.mrc.ac.uk/Softdata/PAX6/Mutations in human PAX6 gene
Gene Identification and StructureHUNThttp://www.hri.co.jp/HUNTAnnotated human full-length cDNA sequences
Mutation DatabasesHvrBasehttp://www.hvrbase.dePrimate mtDNA control region sequences
Gene Identification and StructureHvrBasehttp://www.hvrbase.orgPrimate mtDNA control region sequences
Mutation DatabasesiARC p53 Databasehttp://www.iarc.fr/p53/Missense mutations and small deletions in human p53 reported in peer-reviewed literature
Mutation DatabasesHuman p53/hprt, rodent lacI/lacZ databaseshttp://www.ibiblio.org/dnam/mainpage.htmlMutationsat the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
HOX-PROhttp://www.iephb.nw.ru/labs/lab38/Clustering of homeobox genes
Protein DatabasesooTFDhttp://www.ifti.orgTranscription factors and gene expression
Gene ExpressionMIRAGEhttp://www.ifti.org/Molecular informatics resource for the analysis of gene expression
IMB Jena Image Library of Biological Macromoleculeshttp://www.imb-jena.de/IMAGE.htmlVisualization and analysis of three-dimensional biopolymer structures
The tmRNA Websitehttp://www.indiana.edu/~tmrnatmRNA sequences, foldings, and alignments
Atlas of Genetics and Cytogenetics in Oncology and Haematologyhttp://www.infobiogen.fr/Chromosomal abnormalities in cancer
DBcathttp://www.infobiogen.fr/services/dbcat/Catalog of databases
Genetic and Physical MapsGenetpighttp://www.infobiogen.fr/services/GenetpigGenetic mapping in pig
Genetic and Physical MapsHuGeMaphttp://www.infobiogen.fr/services/HugemapHuman genome genetic and physical map data
Virgilhttp://www.infobiogen.fr/services/virgilDatabase interconnectivity
Genomic DatabasesMouse Genome Database (MGD)http://www.informatics.jax.orgMouse genetics and genomics
Gene Expression Database (GXD)http://www.informatics.jax.org/Mouse gene expression and genomics
Genomic DatabasesIRIShttp://www.iris.irri.orgRice germplasm geneology and field data; rice structural and functional genomics and proteomics
Non-redundant, gene-oriented clusters:H-InvDBhttp://www.jbirc.aist.go.jp/hinv/index.jspHuman gene database, with Integrative Annotation Validated by Full-Length cDNA Clones
JenPephttp://www.jenner.ac.uk/Jenpep2Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules
Gene Identification and StructureCUTGhttp://www.kazusa.or.jp/codon/Codon usage tables
Genomic DatabasesCyanoBasehttp://www.kazusa.or.jp/cyano/Synechocystis sp. genome
Protein DatabasesHUGEhttp://www.kazusa.or.jp/huge/Large (50 kDa) human proteins and cDNA sequences
Haemophila B Mutation Databasehttp://www.kcl.ac.uk/ip/Point mutations, short additions, and deletions in the Factor IX gene
UM-BBDhttp://www.labmed.umn.edu/umbbd/Microbial biocatalytic reactions and biodegradation pathways
Mutation DatabasesHuman Type I and Type III Collagen Mutation Databasehttp://www.le.ac.uk/genetics/collagen/Human type I and type III collagen gene mutations
Lipase Engineering Databasehttp://www.led.uni-stuttgart.de/Integrated information on sequence, structure and function of lipases and esterases
Interferon Stimulated Gene Databasehttp://www.lerner.ccf.org/Genes induced by treatment with interferons
Database of Germline p53 Mutationshttp://www.lf2.cuni.cz/Mutations in human tumor and cell line p53 gene
Genomic DatabasesICBhttp://www.mbio.co.jp/icbIdentification and classification of bacteria using protein-coding
Protein DatabasesRibonuclease P Databasehttp://www.mbio.ncsu.edu/RNaseP/home.htmlRNase P sequences, alignments, and structures
Androgen Receptor Gene Mutations Databasehttp://www.mcgill.ca/androgendb/Mutations in the androgen receptor gene
Genomic DatabasesMtDBhttp://www.medicago.org/MtDBMedicago trunculata genome
Genomic DatabasesMendel Databasehttp://www.mendel.ac.uk/Database of plant EST and STS sequences annotated with gene family information
MEROPShttp://www.merops.co.ukProteolytic enzymes (proteases/peptidases)
Gene ExpressionMethDBhttp://www.methdb.deDNA methylation data, patterns, and profiles
probeBasehttp://www.microbial-ecology.net/rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information
Genomic DatabasesMIPShttp://www.mips.biochem.mpg.de/Protein and genomic sequences
Genomic DatabasesMunich Information Center for Protein Sequences (MIPS)http://www.mips.biochem.mpg.de/Protein and genomic sequences
Genomic DatabasesMITOMAPhttp://www.mitomap.orgHuman mitochondrial genome
Database of Ribosomal Crosslinks (DRC)http://www.mpimg-berlin-dahlem.mpg.de/Ribosomal crosslinking data
Cre Transgenic Databasehttp://www.mshri.on.ca/nagy/Cre transgenic mouse lines
RefSeqhttp://www.ncbi.nih.gov/RefSeq/Reference sequence standards for genomes, genes, transcripts and proteins
International Nucleotide Sequence Database Collaboration:GenBankhttp://www.ncbi.nlm.nih.gov/All known nucleotide and protein sequences
NCBI Taxonomy Browserhttp://www.ncbi.nlm.nih.gov/Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence
Comparative GenomicsClusters of Orthologous Groups (COG)http://www.ncbi.nlm.nih.gov/COG/Phylogenetic classification of proteins from 43 complete genomes
Genetic and Physical MapsGeneMap ’99http://www.ncbi.nlm.nih.gov/genemap/International Radiation Mapping Consortium human gene map
LocusLink/RefSeqhttp://www.ncbi.nlm.nih.gov/LocusLink/Curated sequence and descriptive information about genetic loci
Mutation DatabasesOnline Mendelian Inheritance in Manhttp://www.ncbi.nlm.nih.gov/Omim/Catalog of human genetic and genomic disorders
PathologyBayGenomicshttp://www.ncbi.nlm.nih.gov/Omim/Catalog of human genetic and genomic disorders
PubMedhttp://www.ncbi.nlm.nih.gov/PubMed/MEDLINE and Pre-MEDLINE citations
Mutation DatabasesdbSNPhttp://www.ncbi.nlm.nih.gov/SNP/Single nucleotidepolymorphisms
CDDhttp://www.ncbi.nlm.nih.gov/Structure/Alignment models for conserved protein domains
MMDBhttp://www.ncbi.nlm.nih.gov/Structure/All experimentally-determined three-dimensional structures, linked to NCBI Entrez
Non-redundant, gene-oriented clusters:UniGenehttp://www.ncbi.nlm.nih.gov/UniGene/GenBank sequences partitioned into a non-redundant set
Comparative GenomicsXREFdbhttp://www.ncbi.nlm.nih.gov/XREFdb/Cross-referencing of model organism genetics with mammalian phenotypes
DSDBASEhttp://www.ncbs.res.in/%7Efaculty/Native and modeled disulfide bonds in proteins
Metabolic Pathways and Cellular RegulationPathDBhttp://www.ncgr.org/pathdbBiochemical pathways, compounds and metabolism
Protein DatabasesInBasehttp://www.neb.com/neb/inteins.htmlIntervening protein sequences (inteins) and motifs
Genomic DatabasesMedicago Genome Initiativehttp://www.noble.org/medicago/Model legume Medicago truncatula ESTs, gene expression, and proteomic data
Imprinted Genes and Parent-of-Origin Effectshttp://www.otago.ac.nz/IGCImprinted genes and parent-of-origin effects in animals
Mutation DatabasesPAHdbhttp://www.pahdb.mcgill.ca/Mutations at the phenylalanine hydroxylase locus
LGICdbhttp://www.pasteur.fr/Ligand-gated ion channel subunit sequences
Gene ExpressionPEDBhttp://www.pedb.org/Normal and aberrant prostate gene expression
PathologyPEDBhttp://www.pedb.org/Sequences from prostate tissue and cell type-specific cDNA libraries
The Pharmacogenomics and Pharmacogenetics Knowledge Basehttp://www.pharmgkb.orgVariation in drug response based on human variation
Mutation DatabasesPHEXdbhttp://www.phexdb.mcgill.ca/Mutations in PHEX gene causing X-linked hypophosphatemia
RNA SequencesNoncoding regulatory RNAs databasehttp://www.prl.msu.edu/PLANTncRNAs/Plant non-protein coding RNAs with relevant gene expression information
ISSDhttp://www.protein.bio.msu.su/issd/Integrated sequence and structural information
Proteome BioKnowledge Libraryhttp://www.proteome.comModel organism pathogen, and mammalian proteomes
Protein DatabasesProtoNethttp://www.protonet.cs.huji.ac.il/Hierarchical clustering of SWISS-PROT
PDBhttp://www.rcsb.org/pdb/Structure data determined by X-ray crystallography and NMR
Gene Identification and StructureRTPrimerDBhttp://www.realtimeprimerdatabase.ht.st/Validated PCR primer and probe sequence records
RTPrimerDBhttp://www.realtimeprimerdatabase.ht.st/Validated PCR primer and probe sequence records
Protein DatabasesNRMDhttp://www.receptors.org/NR/An Information System for Nuclear Receptors
RIDOMhttp://www.ridom.de/rRNA (16S and ITS) sequence-based identification of medical microorganisms
RNABasehttp://www.rnabase.orgRNA-containing structures from PDB and NDB
ProThermhttp://www.rtc.riken.go.jp/Thermodynamic data for wild-type and mutant proteins
Non-redundant, gene-oriented clusters:STACKhttp://www.sanbi.ac.za/Dbases.htmlSequences expressed in the human genome
HSSPhttp://www.sander.ebi.ac.uk/hssp/Structural families and alignments; structurally-conserved regions and domain architecture
GB4-RHhttp://www.sanger.ac.uk/Genebridge4 (GB4) human radiation hybrid maps
Genomic DatabasesACeDBhttp://www.sanger.ac.uk/Software/Acedb/C. elegans, S. pombe, and human sequences and genomic information
Protein Sequence MotifsPfamhttp://www.sanger.ac.uk/Software/Pfam/Multiple sequence alignments and hidden Markov models of common protein domains
RNA SequencesRfamhttp://www.sanger.ac.uk/Software/Rfam/Non-coding RNA families
Gene Identification and StructureHS3Dhttp://www.sci.unisannio.it/docenti/rampone/Human exon, intron and splice regions
Gene ExpressionSeedGeneshttp://www.seedgenes.orgGenes essential for Arabidopsis development
Genomic DatabasesOryzabasehttp://www.shigen.nig.ac.jp/rice/oryzabaseRice genetics and genomics
Wnt Databasehttp://www.stanford.edu/Wnt secreted signaling molecules – proteins and phenotypes
Genomic DatabasesArkDBhttp://www.thearkdb.org/species.htmlGenome databases for farm and other animals
Genetic and Physical MapsDRESHhttp://www.tigem.it/LOCAL/drosophila/dros.htmlHuman cDNA clones homologous to Drosophila mutant genes
Comprehensive Microbial Resourcehttp://www.tigr.org/Completed microbial genomes
TIGR Rice Genome Annotation Resourcehttp://www.tigr.org/tdb/e2k1/osa1/Rice sequence, BAC/PAC clones and related mapping data
Human BAC Ends Databasehttp://www.tigr.org/tdb/humgen/Non-redundant human BAC end sequences
Non-redundant, gene-oriented clusters:TIGR Gene Indiceshttp://www.tigr.org/tdb/index.shtmlMicrobes, plants and humans
TIGR Microbial Databasehttp://www.tigr.org/tdb/mdb/mdbcomplete.htmlMicrobial genomes and chromosomes
Protein DatabasesTIGRFAMshttp://www.tigr.org/TIGRFAMsProtein family resource for the functional identification of proteins
TOPShttp://www.tops.leeds.ac.uk/Topology of protein structure
PathologyOral Cancer Gene Databasehttp://www.tumor-gene.org/Oral/oral.htmlCellular, molecular, and biological data for genes involved in oral cancer
PathologyTumor Gene Family Databases (TGDBs)http://www.tumor-gene.org/tgdf.htmlCellular, molecular, and biological data about genes involved in various cancers
Mutation DatabasesNCL Mutationshttp://www.ucl.ac.uk/ncl/Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
PathologyPGDBhttp://www.ucsf.edu/pgdb/index.htmGenes and genomic loci related to the prostate and prostatic diseases
tRNA Sequenceshttp://www.uni-bayreuth.de/tRNA and tRNA gene sequences
Gene Identification and StructureWormBasehttp://www.wormbase.orgGuide to C. elegans biology
WormBasehttp://www.wormbase.orgGenomic data on C. elegans and related nematodes
ZFINhttp://www.zfin.orgGenetic, genomic and developmental data from zebrafish
Protein Sequence MotifsSBASEhttp://www3.icgeb.trieste.it/~sbasesrv/Annotated protein domain sequences
HOWDYhttp://www-alias.tokyo.jst.go.jp/HOWDY/Integrated human genomic information
Pseudobasehttp://wwwbio.leidenuniv.nl/Information on RNA pseudoknots
SLoophttp://www-cryst.bioc.cam.ac.uk/~sloop/Classification of protein loops
BAliBASEhttp://www-igbmc.u-strasbg.fr/Benchmark database for comparison of multiple sequence alignments
Genomic DatabasesMitoDathttp://www-lecb.ncifcrf.gov/mitoDat/Mitochondrial proteins (predominantly human)
ACTIVITYhttp://wwwmgs.bionet.nsc.ru/Functional DNA/RNA site activity
SELEXdbhttp://wwwmgs.bionet.nsc.ru/Selected DNA/RNA functional site sequences
Gene Identification and StructureTRRDhttp://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/Transcription regulatory regions of eukaryotic genes
Protein DatabasesASPDhttp://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/Artificial selected proteins/peptides database
Gene Identification and StructurerSNP Guidehttp://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/Single nucleotide polymorphisms in regulatory gene regions
PIR-ALNhttp://www-nbrf.georgetown.edu/Protein sequence alignments
RESIDhttp://www-nbrf.georgetown.edu/Protein structure modifications
Genetic and Physical MapsG3-RHhttp://www-shgc.stanford.edu/RH/Stanford G3 and TNG radiation hybrid maps
LPFChttp://www-smi.stanford.edu/Library of protein family core structures
Protein DatabasesSENTRAhttp://www-wit.mcs.anl.gov/sentra/Sensory signal transduction proteins
Genomic DatabasesPhytophora Genome Consortium Databasehttp://xgi.ncgr.org/pgcESTs from Phytophthora infestans and Phytophthora sojae
KDBIhttp://xin.cz3.nus.edu.sg/group/kdbi/kdbi.aspKintic data on biomolecular interactions
HIC-Uphttp://xray.bmc.uu.se/hicup/Structures of small molecules (hetero-compounds)
TRIPLEShttp://ygac.med.yale.edu/triples/triples.htmTRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
ZmDBhttp://zmdb.iastate.edu/Maize genome database
Genomic DatabasesPlantGDBhttp://zmdb.iastate.edu/PlantGDB/Actively-transcribed plant genomic sequences
Genomic DatabasesASAPhttps://asap.ahabs.wisc.edu/annotation/ASAP1.htmSystematic annotation package for community-based annotation and analysis of genomes