UHH > F'ty Biology > Links > Databases	search

Links to Databases for Molecular Biologists
Global Sequence Databases
International Nucleotide Sequence Database Collaboration:
	DNA Data Bank of Japan (DDBJ)		http://www.ddbj.nig.ac.jp		All known nucleotide and protein sequences
	EMBL Nucleotide Sequence Database		http://www.ebi.ac.uk/embl/		All known nucleotide and protein sequences
	GenBank		http://www.ncbi.nlm.nih.gov/		All known nucleotide and protein sequences
Non-redundant, gene-oriented clusters:
	NCBI Reference Sequence Project		http://www.ncbi.nlm.nih.gov./RefSeq/		Naturally-occuring biological molecules
	H-InvDB		http://www.jbirc.aist.go.jp/hinv/index.jsp		Human gene database, with Integrative Annotation Validated by Full-Length cDNA Clones
	STACK		http://www.sanbi.ac.za/Dbases.html		Sequences expressed in the human genome
	TIGR Gene Indices		http://www.tigr.org/tdb/index.shtml		Microbes, plants and humans
	UniGene		http://www.ncbi.nlm.nih.gov/UniGene/		GenBank sequences partitioned into a non-redundant set
	Ensembl		http://www.ensembl.org		Annotated information on eukaryotic genomes
	UCSC Genome Browser		http://genome.ucsc.edu/		Genome assemblies and annotation
Comparative Genomics
	Clusters of Orthologous Groups (COG)		http://www.ncbi.nlm.nih.gov/COG/		Phylogenetic classification of proteins from 43 complete genomes
	CORG		http://corg.molgen.mpg.de		Conserved non-coding sequence blocks
	Homophila		http://homophila.sdsc.edu		Relationship of human disease genes to genes in Drosophila
	MBGD		http://mbgd.genome.ad.jp		Microbial genome database for comparative genomic analysis
	ParaDB		http://abi.marseille.inserm.fr/paradb		Paralogy mapping in human genomes
	XREFdb		http://www.ncbi.nlm.nih.gov/XREFdb/		Cross-referencing of model organism genetics with mammalian phenotypes
Gene Expression
	ArrayExpress		http://www.ebi.ac.uk.arrayexpress		Public collection of microarray gene expression data
	ASDB		http://cbcg.nersc.gov/asdb		Protein products and expression patterns of alternatively-spliced genes
	Axeldb		http://www.dkfz-heidelberg.de/ abt0135/axeldb.htm		Gene expression in Xenopus
	BodyMap		http://bodymap.ims.u-tokyo.ac.jp/		Human and mouse gene expression data
	EPConDB		http://www.cbil.upenn.edu/EPConDB		Endocrine pancreas consortium database
	EpoDB		http://www.cbil.upenn.edu/EpoDB/index.html		Genes expressed in vertebrate red blood cells
	FlyView		http://pbio07.uni-muenster.de/		Drosophila development and genetics
	Gene Expression Database (GXD)		http://www.informatics.jax.org/ searches/gxdindex_form.shtml		Mouse gene expression and genomics
	HugeIndex		http://hugeindex.org		mRNA expression levels of human genes in normal tissues
	Interferon Stimulated Gene Database		http://www.lerner.ccf.org/ labs/williams/xchip-html.cgi		Genes induced by treatment with interferons
	Kidney Development Database		http://golgi.ana.ed.ac.uk/kidhome.html		Kidney development and gene expression
	MAGEST		http://www.genome.ad.jp/magest/		Maboya ( the ascidian, Halocynthia roretzi ) Gene Expression patterns and Sequence Tags
	MEPD		http://medaka.dsp.jst.go.jp/MEPD		Gene expression data from the small freshwater fish Medaka
	MethDB		http://www.methdb.de		DNA methylation data, patterns, and profiles
	MIRAGE		http://www.ifti.org/		Molecular informatics resource for the analysis of gene expression
	Mouse Atlas and Gene Expression Database		http://genex.hgu.mrc.ac.uk		Spatially-mapped gene expression data
	MTID		http://mouse.ccgb.umn.edu/transposon/		Sleeping beauty transposon insertion in mice
	NetAffix		http://www.affymetrics.com		Public Affymetrix probesets and annotations
	PEDB		http://www.pedb.org/		Normal and aberrant prostate gene expression
	RECODE		http://recode.genetics.utah.edu		Genes using programmed translational recoding in their expression
	SeedGenes		http://www.seedgenes.org		Genes essential for Arabidopsis development
	Stanford Microarray Database		http://genome-www.stanford.edu/microarray		Raw and normalized data from microarray experiments
	Tooth Development Database		http://bite-it.helsinki.fi/		Gene expression in dental tissue
	TRANSPATH		http://www.biobase.de/pages/ products/databases.html		Gene regulatory networks and microarray analysis
	TRIPLES		http://ygac.med.yale.edu/triples/triples.htm		TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
Gene Identification and Structure
	AllGenes		http://www.allgenes.org		Human and mouse gene index integrating gene, transcript and protein annotation
	Ares Lab Intron Site		http://www.cse.ucsc.edu/research/ compbio/yeast_introns.html		Yeast spliceosomal introns
	ASAP		http://www.bioinformatics.ucla.edu/ASAP		Alternative spliced isoforms
	COMPEL		http://compel.bionet.nsc.ru/		Database on composite regulatory elements affecting gene transcription in eukaryotes
	CUTG		http://www.kazusa.or.jp/codon/		Codon usage tables
	DBTBS		http://elmo.ims.u-tokyo.ac.jp/dbtbs/		Bacillus subtilis promoters and transcription factors
	EID		http://mcb.harvard.edu/gilbert/EID/		Protein-coding, intron-containing genes
	EPD		http://www.epd.isb-sib.ch/		Eukaryotic POL II promoters with experimentally-determined transcription start sites
	ExInt		http://intron.bic.nus.edu.sg/exint/exint.html		Exon-intron structure of eukaryotic genes
	Gene Resource Locator		http://grl.gi.u-tokyo.ac.jp		Alignment of ESTs with finished human sequence
	HS3D		http://www.sci.unisannio.it/docenti/rampone/		Human exon, intron and splice regions
	HUNT		http://www.hri.co.jp/HUNT		Annotated human full-length cDNA sequences
	HvrBase		http://www.hvrbase.org		Primate mtDNA control region sequences
	IDB/IEDB		http://nutmeg.bio.indiana.edu/intron/index.html		Intron sequence and evolution
	MICdb		http://www.cdfd.org.in/micas		Prokaryotic microsattelites
	PACRAT		http://www.biosci.ohio-state.edu/~pacrat		Archaeal and bacterial intergenic sequence features
	PLACE		http://www.dna.affrc.go.jp/htdocs/PLACE		Plant cis-acting regulatory elements
	PlantCARE		http://oberon.rug.ac.be:8080/PlantCARE/index.html		Plant transcription sites
	PlantProm		http://mendel.cs.rhul.ac.uk/		Proximal promoter sequences for RNA polymerase II
	PromEC		http://bioinfo.md.huji.ac.il/marg/promec		E. coli mRNA promoters with experimentally identified transcriptional start sites
	RRNDB		http://rrndb.cme.msu.edu		Variation in prokaryotic ribosomal RNA operons
	rSNP Guide		http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/		Single nucleotide polymorphisms in regulatory gene regions
	RTPrimerDB		http://www.realtimeprimerdatabase.ht.st/		Validated PCR primer and probe sequence records
	SNP Consortium database		http://snp.cshl.org		Single Nucleotide Polymorphisms for biomedical research
	Sputnik		http://mips.gsf.de/proj/sputnik		Functional annotation of clustered plant ESTs
	STRBase		http://www.cstl.nist.gov/div831/strbase/		Short tandem DNA repeats
	TRANSCompel		http://www.gene-regulation.com/pub/ databases.html#transcompel		Composite regulatory elements
	TransTerm		http://uther.otago.ac.nz/Transterm.html		Codon usage, start and stop signals
	TRRD		http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/		Transcription regulatory regions of eukaryotic genes
	VIDA		http://www.biochem.ucl.ac.uk/ bsm/virus_database/VIDA.html		Virus genome open reading frames
	WormBase		http://www.wormbase.org		Guide to C. elegans biology
Genetic and Physical Maps
	DRESH		http://www.tigem.it/LOCAL/drosophila/dros.html		Human cDNA clones homologous to Drosophila mutant genes
	G3-RH		http://www-shgc.stanford.edu/RH/		Stanford G3 and TNG radiation hybrid maps
	GB4-RH		http://www.sanger.ac.uk/ Software/RHserver//RHserver.shtml		Genebridge4 (GB4) human radiation hybrid maps
	GDB		http://www.gdb.org		Human genes and genomic maps
	GenAtlas		http://www.dsi.univ-paris5.fr/genatlas/		Human genes, markers, and phenotypes
	GeneLoc		http://genecards.weizmann.ac.il/udb/		Integrated human maps
	GeneMap '99		http://www.ncbi.nlm.nih.gov/genemap/		International Radiation Mapping Consortium human gene map
	Genetpig		http://www.infobiogen.fr/services/Genetpig		Genetic mapping in pig
	GenMapDB		http://genomics.med.upenn.edu/genmapdb		Mapped human BAC clones
	HuGeMap		http://www.infobiogen.fr/services/Hugemap		Human genome genetic and physical map data
	IXDB		http://ixdb.mpimg-berlin-dahlem.mpg.de		Physical maps of human chromosome X
	RHdb		http://www.ebi.ac.uk/RHdb		Radiation hybrid map data
Genomic Databases
	ACeDB		http://www.sanger.ac.uk/Software/Acedb/		C. elegans, S. pombe, and human sequences and genomic information
	AMmtDB		http://bighost.area.ba.cnr.it/mitochondriome		Metazoan mitochondrial genes
	ArkDB		http://www.thearkdb.org/species.html		Genome databases for farm and other animals
	ASAP		https://asap.ahabs.wisc.edu/annotation/ASAP1.htm		Systematic annotation package for community-based annotation and analysis of genomes
	BSD		http://bsd.cme.msu.edu		Comparative data on known biodegradative organisms
	CATMA		http://www.catma.org		Arabidopsis gene sequence tags (GSTs)
	CnidBase		http://cnidbase.bu.edu/		Cnidarian evolutionary genomics and gene expression
	Comprehensive Microbial Resource		http://www.tigr.org/ tigr-scripts/CMR2/CMRHomePage.spl		Completed microbial genomes
	CropNet		http://ukcrop.net/		Genome mapping in crop plants
	CroW 21		http://bioinfo.weizmann.ac.il/crow21/		Human chromosome 21 database
	CyanoBase		http://www.kazusa.or.jp/cyano/		Synechocystis sp. genome
	EcoGene		http://bmb.med.miami.edu/EcoGene/EcoWeb/		E. coli K-12 sequences
	EMGlib		http://pbil.univ-lyon1.fr/emglib/emglib.html		Completely sequenced microbial genomes from bacteria, archaea, yeast
	ERGO		http://ergo.integratedgenomics.com/ERGO		Integrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature
	FlyBase		http://www.fruitfly.org		Drosophila sequences and genomic information
	Full-Malaria		http://fullmal.ims.u-tokyo.ac.jp		Full-length cDNA library from erythrocytic-stage Plasmodium falciparum
	GeneCards		http://bioinfo.weizmann.ac.il/cards		Integrated database of human genes, maps, proteins and diseases
	Genew		http://www.gene.ucl.ac.uk./cgi-bin/ nomenclature/searchgenes.pl		Approved symbols for all human genes
	GOBASE		http://megasun.bch.umontreal.ca/ gobase/gobase.html		Organelle genome database
	GOLD		http://igweb.integratedgenomics.com/GOLD/		Information regarding complete and ongoing genome projects
	GénoPlante-Info		http://genoplante-info.infobiogen.fr		Plant genomic data derived from the Génoplante consortium
	GrainGenes		http://www.graingenes.org		Genomic database for small-grain crops
	HGT-DB		http://www.fut.es/~debb/HGT/		Putative horizontally-transferred genes in prokaryotic genomes
	HIV Sequence Database		http://hiv-web.lanl.gov/		HIV RNA sequences
	HOWDY		http://www-alias.tokyo.jst.go.jp/HOWDY/		Integrated human genomic information
	Human BAC Ends Database		http://www.tigr.org/tdb/humgen/ bac_end_search/bac_end_intro.html		Non-redundant human BAC end sequences
	ICB		http://www.mbio.co.jp/icb		Identification and classification of bacteria using protein-coding
	INE		http://rgp.dna.affrc.go.jp/giot/INE.html		Rice genetic and physical maps and sequence data
	IRIS		http://www.iris.irri.org		Rice germplasm geneology and field data; rice structural and functional genomics and proteomics
	Medicago Genome Initiative		http://www.noble.org/medicago/		Model legume Medicago truncatula ESTs, gene expression, and proteomic data
	Mendel Database		http://www.mendel.ac.uk/		Database of plant EST and STS sequences annotated with gene family information
	MIPS		http://www.mips.biochem.mpg.de/		Protein and genomic sequences
	MitoDat		http://www-lecb.ncifcrf.gov/mitoDat/		Mitochondrial proteins (predominantly human)
	MITOMAP		http://www.mitomap.org		Human mitochondrial genome
	MitoNuc/MitoAln		http://bighost.area.ba.cnr.it/srs/		Nuclear genes coding for mitochondrial proteins
	MITOP		http://mips.gsf.de/proj/medgen/mitop/		Mitochondrial proteins, genes, and diseases
	MOsDB		http://mips.gsf.de/proj/rice		Oryza sativa genome
	Mouse Genome Database (MGD)		http://www.informatics.jax.org		Mouse genetics and genomics
	MtDB		http://www.medicago.org/MtDB		Medicago trunculata genome
	Munich Information Center for Protein Sequences (MIPS)		http://www.mips.biochem.mpg.de/		Protein and genomic sequences
	NRSub		http://pbil.univ-lyon1.fr/nrsub/nrsub.html		Bacillus subtilis genome
	OGRe		http://www.bioinf.man.ac.uk/ogre		Complete mitochondrial genome sequences for 200 metazoan species
	Oryzabase		http://www.shigen.nig.ac.jp/rice/oryzabase		Rice genetics and genomics
	PEDANT genome database		http://pedant.gsf.de		Automated analysis of genomic sequences
	Phytophora Genome Consortium Database		http://xgi.ncgr.org/pgc		ESTs from Phytophthora infestans and Phytophthora sojae
	PlantGDB		http://zmdb.iastate.edu/PlantGDB/		Actively-transcribed plant genomic sequences
	PlasmoDB		http://PlasmoDB.org		The Plasmodium falciparum Genome Database
	Proteome BioKnowledge Library		http://www.proteome.com		Model organism pathogen, and mammalian proteomes
	Rat Genome Database		http://rgd.mcw.edu		Rat genetic and genomic data
	Rice GAAS		http://RiceGaas.dna.affrc.go.jp/		Rice genome sequence
	RsGDB		http://mmg.uth.tmc.edu/sphaeroides		Rhodobacter sphaeroides genome
	RTPrimerDB		http://www.realtimeprimerdatabase.ht.st/		Validated PCR primer and probe sequence records
	Saccharomyces Genome Database (SGD)		http://genome-www.stanford.edu/Saccharomyces		Saccharomyces cerevisiae genome
	SOURCE		http://source.stanford.edu		Functional genomic resource for annotations ontologies, and expression data
	SubtiList		http://genolist.pasteur.fr/SubtiList		Bacillus subtilis genome
	The Arabidopsis Information Resource (TAIR)		http://www.arabidopsis.org		Arabidopsis thaliana genome
	TIGR Microbial Database		http://www.tigr.org/tdb/mdb/mdbcomplete.html		Microbial genomes and chromosomes
	TIGR Rice Genome Annotation Resource		http://www.tigr.org/tdb/e2k1/osa1/		Rice sequence, BAC/PAC clones and related mapping data
	ToxoDB: The Toxoplasma gondii Genome Database		http://ToxoDB.org		Apicomplexan parasite Toxoplasma gondii genome
	WILMA		http://lore.came.sbg.ac.at:8080/ CAME/CAME_EXTERN/WILMA/		Caenorhabditis elegans annotation
	WorfDB		http://worf.dfci.harvard.edu		Caenorhabditis elegans ORFeome
	WormBase		http://www.wormbase.org		Genomic data on C. elegans and related nematodes
	ZFIN		http://www.zfin.org		Genetic, genomic and developmental data from zebrafish
	ZmDB		http://zmdb.iastate.edu/		Maize genome database
Intermolecular Interactions
	Biomolecular Interaction Network Database (BIND)		http://binddb.org		Molecular interactions, complexes, and pathways
	DIP		http://dip.doe-mbi.ucla.edu/		Catalog of protein-protein interactions
	Database of Ribosomal Crosslinks (DRC)		http://www.mpimg-berlin-dahlem.mpg.de/ ~ag_ribo/ag_brimacombe/drc/		Ribosomal crosslinking data
	DPInteract		http://arep.med.harvard.edu/dpinteract/		Binding sites for E. coli DNA-binding proteins
	InterDom		http://InterDom.lit.org.sg		Putative protein domain interactions
	JenPep		http://www.jenner.ac.uk/Jenpep2		Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules
	KDBI		http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp		Kintic data on biomolecular interactions
	MHC-Peptide Interaction Database		http://surya.bic.nus.edu.sg/mpid		Class I and class II MHC-peptide complexes
	STRING		http://www.bork.embl-heidelberg.de/STRING/		Predicted functional associations between proteins
Metabolic Pathways and Cellular Regulation
	EcoCyc		http://ecocyc.org/		E. coli K-12 genome, gene products, and metabolic pathways
	ENZYME		http://www.expasy.ch/enzyme/		Enzyme nomenclature
	EpoDB		http://www.cbil.upenn.edu/EpoDB/		Genes expressed during human erythropoiesis
	Klotho		http://www.biocheminfo.org/klotho		Collection and categorization of biological compounds
	Kyoto Encyclopedia of Genes and Genomes (KEGG)		http://www.genome.ad.jp/kegg/		Metabolic and regulatory pathways
	LIGAND		http://www.genome.ad.jp/dbget/ligand.html		Enzymatic ligands, substrates, and reactions
	MetaCyc		http://ecocyc.org		Metabolic pathways and enzymes from various organisms
	The University of Minnesota Biocatalysis Biodegradation Database		http://umbbd.ahc.umn.edu/		Curated information on microbial catabolism and related biotransformations
	PathDB		http://www.ncgr.org/pathdb		Biochemical pathways, compounds and metabolism
	PRODORIC		http://prodoric.tu-bs.de		Prokaryotic database of gene regulation and regulatory networks
	RegulonDB		http://www.cifn.unam.mx/ Computational_Genomics/regulondb/		E. coli transcriptional regulation and operon organization
	UM-BBD		http://www.labmed.umn.edu/umbbd/		Microbial biocatalytic reactions and biodegradation pathways
	WIT2		http://wit.mcs.anl.gov/WIT2/		Integrated system for functional curation and development of metabolic models
Mutation Databases
	ALFRED		http://alfred.med.yale.edu/ alfred/index.asp		Allele frequencies and DNA polymorphisms
	Androgen Receptor Gene Mutations Database		http://www.mcgill.ca/androgendb/		Mutations in the androgen receptor gene
	Asthma Gene Database		http://cooke.gsf.de/asthmagen/main.cfm		Linkage and mutation studies on the genetics of asthma and allergy
	Atlas of Genetics and Cytogenetics in Oncology and Haematology		http://www.infobiogen.fr/ services/chromcancer/		Chromosomal abnormalities in cancer
	BTKbase		http://bioinf.uta.fi/BTKbase/		Mutation registry for X-linked agammaglobulinemia
	CASRDB		http://www.casrdb.mcgill.ca/		Calcium Sensing Receptor Locus Mutation Database
	Cytokine Gene Polymorphism Database		http://www.bris.ac.uk/pathandmicro/ services/GAI/cytokine4.htm		Cytokine gene polymorphisms, in vitro expression and disease-association studies
	Database of Germline p53 Mutations		http://www.lf2.cuni.cz/ win/projects/germline_mut_p53.htm		Mutations in human tumor and cell line p53 gene
	dbSNP		http://www.ncbi.nlm.nih.gov/SNP/		Single nucleotidepolymorphisms
	FLAGdb/FST		http://genoplante-info.infobiogen.fr		Arabidopsis thaliana T-DNA transformants
	GRAP Mutant Databases		http://tinyGRAP.uit.no/GRAP/		Mutants of family A G-Protein Coupled Receptors (GRAP)
	Haemophila B Mutation Database		http://www.kcl.ac.uk/ip/ petergreen/haemBdatabase.html		Point mutations, short additions, and deletions in the Factor IX gene
	HGVbase		http://hgvbase.cgb.ki.se/		Human Genome Variation database
	HIV-RT		http://hivdb.stanford.edu/hiv/		HIV reverse transcriptase and protease sequence variation
	Human Gene Mutation Database (HGMD)		http://www.hgmd.org		Known (published) gene lesions underlying human inherited disease
	Human p53/hprt, rodent lacI/lacZ databases		http://www.ibiblio.org/dnam/mainpage.html		Mutationsat the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
	Human PAX2 Allelic Variant Database		http://www.hgu.mrc.ac.uk/Softdata/PAX2/		Mutations in human PAX2 gene
	Human PAX6 Allelic Variant Database		http://www.hgu.mrc.ac.uk/Softdata/PAX6/		Mutations in human PAX6 gene
	Human Type I and Type III Collagen Mutation Database		http://www.le.ac.uk/genetics/collagen/		Human type I and type III collagen gene mutations
	HvrBase		http://www.hvrbase.de		Primate mtDNA control region sequences
	iARC p53 Database		http://www.iarc.fr/p53/		Missense mutations and small deletions in human p53 reported in peer-reviewed literature
	KinMutBase		http://bioinf.uta.fi/KinMutBase/		Disease-causing protein kinase mutations
	Mutation Spectra Database		http://info.med.yale.edu/mutbase/		Mutations in viral, bacterial, yeast, and mammalian genes
	NCL Mutations		http://www.ucl.ac.uk/ncl/		Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
	Online Mendelian Inheritance in Animals		http://www.angis.org.au/omia		Catalog of animal genetic and genomic disorders
	Online Mendelian Inheritance in Man		http://www.ncbi.nlm.nih.gov/Omim/		Catalog of human genetic and genomic disorders
	p53 Databases		http://metalab.unc.edu/dnam/mainpage.html		Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
	PAHdb		http://www.pahdb.mcgill.ca/		Mutations at the phenylalanine hydroxylase locus
	PHEXdb		http://www.phexdb.mcgill.ca/		Mutations in PHEX gene causing X-linked hypophosphatemia
	PMD		http://pmd.ddbj.nig.ac.jp/		Compilation of protein mutant data
	PTCH Mutation Database		http://www.cybergene.se/PTCH/ptchbase.html		Mutations and SNPs found in PTCH1
	RB1 Gene Mutation Database		http://www.d-lohmann.de/Rb/		Mutations in the human retinoblastoma (RB1) gene
	SV40 Large T-Antigen Mutant Database		http://colon.bio.pitt.edu:5243/SV40/index.html		Mutations in SV40 large tumor antigen gene
Pathology
	BayGenomics		http://www.ncbi.nlm.nih.gov/Omim/		Catalog of human genetic and genomic disorders
	FIMM		http://baygenomics.ucsf.edu		Identification of genes relevant to cardiovascular and pulmonary disease
	GOLD.db		http://gold.tugraz.at		Genes, proteins, and pathways implicated in lipid-associated disorders
	INFEVERS		http://fmf.igh.cnrs.fr/infevers		Familial Mediterranean Fever and hereditary inflammatory disorder mutation data
	MetaFMF		http://fmf.igh.cnrs.fr/metaFMF/index_us.html		Familial Mediterranean Fever phenotype-genotype correlation
	Mouse Tumor Biology Database (MTB)		http://tumor.informatics.jax.org		Mouse tumor names, classification, incidence, pathology, genetic factors
	Oral Cancer Gene Database		http://www.tumor-gene.org/Oral/oral.html		Cellular, molecular, and biological data for genes involved in oral cancer
	PEDB		http://www.pedb.org/		Sequences from prostate tissue and cell type-specific cDNA libraries
	PGDB		http://www.ucsf.edu/pgdb/index.htm		Genes and genomic loci related to the prostate and prostatic diseases
	Tumor Gene Family Databases (TGDBs)		http://www.tumor-gene.org/tgdf.html		Cellular, molecular, and biological data about genes involved in various cancers
Protein Databases
	AARSDB		http://rose.man.poznan.pl/aars/index.html		Aminoacyl-tRNA synthetase sequences
	ABCdb		http://ir2lcb.cnrs-mrs.fr/ABCdb/		ABC transporters
	AraC/XylS database		http://www.AraC-XylS.org		AraC/XylS protein family of positive regulators in bacteria
	ASPD		http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/		Artificial selected proteins/peptides database
	CSDBase		http://www.chemie.uni-marburg.de/~csdbase		Cold shock domain-containing proteins
	DAtA		http://luggagefast.Stanford.EDU/ group/arabprotein/		Annotated coding sequences from Arabidopsis
	DExH/D Family Database		http://www.helicase.net/dexhd/dbhome.htm		DEAD-box, DEAH-box, and DExH-box proteins
	Endogenous GPCR List		http://www.biomedcomp.com/GPCR.html		G protein-coupled receptors; expression in cell lines
	ESTHER		http://bioweb.ensam.inra.fr/ESTHER/ general?what=index		Esterases and alpha/beta hydrolase enzymes and relatives
	EXProt		http://www.cmbi.nl/exprot		Proteins with experimentally-verified function
	FUNPEP		http://www.cmbi.kun.nl/swift/FUNPEP/library/		Low-complexity or compositionally-biased protein sequences
	GenProtEC		http://genprotec.mbl.edu		Escherichia coli K-12 genome, gene products, and homologs
	GPCRDB		http://www.gpcr.org/7tm/		G protein-coupled receptors
	Histone Database		http://genome.nhgri.nih.gov/histones/		Histone and histone fold sequences and structures
	HIV Molecular Immunology Database		http://hiv-web.lanl.gov/immunology/		HIV epitopes
	HIV RT and Protease Sequence Database		http://hivdb.stanford.edu		HIV reverse transcriptase and protease sequences
	Homeobox Page		http://homeobox.biosci.ki.se		Information relevant to homeobox proteins, classification, and evolution
	Homeodomain Resource		http://genome.nhgri.nih.gov/homeodomain		Homeodomain sequences, structures, and related genetic and genomic information
	HORDE		http://bioinfo.weizmann.ac.il/HORDE/		Catalog of human genetic and genomic disorders
	HUGE		http://www.kazusa.or.jp/huge/		Large (50 kDa) human proteins and cDNA sequences
	IMGT		http://imgt.cines.fr:8104/		Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
	IMGT/HLA		http://www.ebi.ac.uk/imgt/hla/		Human major histocompatibility comples
	IMGT/MHC Database		http://www.ebi.ac.uk/imgt/mhc		Major histocompatibility complex sequences
	InBase		http://www.neb.com/neb/inteins.html		Intervening protein sequences (inteins) and motifs
	InterPro		http://www.ebi.ac.uk/interpro		Protein families and domains
	Kabat Database		http://immuno.bme.nwu.edu/		Sequences of proteins of immunological interest
	LGICdb		http://www.pasteur.fr/ recherche/banques/LGIC/LGIC.html		Ligand-gated ion channel subunit sequences
	Lipase Engineering Database		http://www.led.uni-stuttgart.de/		Integrated information on sequence, structure and function of lipases and esterases
	MEROPS		http://www.merops.co.uk		Proteolytic enzymes (proteases/peptidases)
	MetaFam		http://metafam.ahc.umn.edu/		Integrated protein family information
	Metalloprotein Database and Browser		http://metallo.scripps.edu/		Metal-binding sites in metalloproteins
	MHCPEP		http://wehih.wehi.edu.au/mhcpep/		MHC-binding peptides
	MitoDrome		http://bighost.area.ba.cnr.it/BIG/MitoDrome		Drosophila nuclear genes encoding proteins targeted to the mitochondrion
	MPIMP		http://millar3.biochem.uwa.edu.au/ ~lister/index.html		Mitochondrial protein import machinery of plants
	Nuclear Protein Database (NPD)		http://npd.hgu.mrc.ac.uk		Proteins localized in the nucleus
	NRMD		http://www.receptors.org/NR/		An Information System for Nuclear Receptors
	Nuclear Receptor Resource		http://nrr.georgetown.edu/nrr/nrr.html		Nuclear receptor superfamily
	NUREBASE		http://www.ens-lyon.fr/LBMC/ laudet/nurebase.html		Nuclear Receptor dataBase
	Olfactory Receptor Database		http://senselab.med.yale.edu/senselab/		Sequences for olfactory receptor-like molecules
	ooTFD		http://www.ifti.org		Transcription factors and gene expression
	PANTHER		http://panther.celera.com		Gene products organized by biological function
	Peptaibol		http://www.cryst.bbk.ac.uk/ peptaibol/welcome.html		Peptaibol (antibiotic peptide) sequences
	PhosphoBase		http://www.cbs.dtu.dk/ databases/PhosphoBase/		Protein phosphorylation sites
	PIR-NREF		http://pir.georgetown.edu/pirwww/pirnref.shtml		Non-redundant reference database with comprehensive protein sequences
	PKR		http://pkr.sdsc.edu/html/index.shtml		Protein kinase sequences, enzymology, genetics, and molecular and structural properties
	PlantsP/PlantsT		http://plantsp.sdsc.edu		Functional genomics databases focusing on protein involved in plant phosphorylation and membrane transport
	PPMdb		http://sphinx.rug.ac.be:8080/ ppmdb/index.html		Arabidopsis plasma membrane protein sequence and expression data
	Prolysis		http://delphi.phys.univ-tours.fr/Prolysis/		Proteases and natural and synthetic protease inhibitors
	PROMISE		http://metallo.scripps.edu/PROMISE/		Prosthetic centers and metal ions in protein active sites
	Protein Information Resource (PIR)		http://pir.georgetown.edu		Comprehensive, annotated, non-redundant protein sequence database
	ProtoNet		http://www.protonet.cs.huji.ac.il/		Hierarchical clustering of SWISS-PROT
	Ribonuclease P Database		http://www.mbio.ncsu.edu/RNaseP/home.html		RNase P sequences, alignments, and structures
	RTKdb		http://pbil.univ-lyon1.fr/RTKdb		Receptor tyrosine kinase sequences
	SDAP		http://fermi.utmb.edu/SDAP		Sequences, structures and IgE epitopes of allergenic proteins
	SENTRA		http://www-wit.mcs.anl.gov/sentra/		Sensory signal transduction proteins
	SEVENS		http://sevens.cbrc.jp		7-transmembrane helix receptors
	SRPDB		http://bio.lundberg.gu.se/dbs/ SRPDB/SRPDB.html		Structural and functional information on signalrecognition particles
	SWISS-PROT/TrEMBL		http://www.expasy.ch/sprot		Curated protein sequences
	TIGRFAMs		http://www.tigr.org/TIGRFAMs		Protein family resource for the functional identification of proteins
	TRANSFAC		http://transfac.gbf.de/TRANSFAC/index.html		Transcription factors and binding sites
	trEST, trGEN and Hits		http://hits.isb-sib.ch		Predicted protein sequences
	VIDA		http://www.biochem.ucl.ac.uk/bsm/ virus_database/VIDA.html		Homologous viral protein families
	Wnt Database		http://www.stanford.edu/ ~rnusse/wntwindow.html		Wnt secreted signaling molecules - proteins and phenotypes
Protein Sequence Motifs
	ASC-Active Sequence Collection		http://crisceb.unina2.it/ASC/		Biologically-active short amino acid sequences
	BLOCKS		http://blocks.fhcrc.org/		Conserved sequence regions of protein families
	CDD		http://www.ncbi.nlm.nih.gov/Structure/ cdd/cdd.shtml		Alignment models for conserved protein domains
	CluSTr		http://www.ebi.ac.uk/clustr/		Automatic classification of SWISS-PROT + TrEMBL proteins into related groups
	eMOTIF		http://motif.stanford.edu/emotif		Protein sequence motif determination and searches
	InterPro		http://www.ebi.ac.uk/interpro/		Integrated documentation resource for protein families, domains, and sites
	iPROCLASS		pir.georgetown.edu/iproclass/		Annotated protein classification database
	NESbase		http://www.cbs.dtu.dk/databases/NESbase		Nuclear export signals
	NLSdb		http://cubic.bioc.columbia.edu/db/NLSdb		Nuclear localization signals
	O-GLYCBASE		http://www.cbs.dtu.dk/databases/OGLYCBASE/		Glycoproteins and O-linked glycosylation sites
	Pfam		http://www.sanger.ac.uk/Software/Pfam/		Multiple sequence alignments and hidden Markov models of common protein domains
	PIR-ALN		http://www-nbrf.georgetown.edu/ pirwww/dbinfo/piraln.html		Protein sequence alignments
	PRINTS		http://www.bioinf.man.ac.uk/ dbbrowser/PRINTS/		Hierarchical gene family fingerprints
	ProClass		http://pir.georgetown.edu/ gfserver/proclass.html		Protein families defined by PIR superfamilies and PROSITE patterns
	ProDom		http://prodes.toulouse.inra.fr/prodom/ 2002.1/html/home.php		Protein domain families
	PROSITE		http://www.expasy.ch/prosite/		Biologically-significant protein patterns and profiles
	ProtoMap		http://protomap.cornell.edu		Automated hierarchical classification of SWISS-PROT proteins
	SBASE		http://www3.icgeb.trieste.it/~sbasesrv/		Annotated protein domain sequences
	SMART		http://smart.embl-heidelberg.de/		Signalling domain sequences
	SUPFAM		http://pauling.mbu.iisc.ernet.in/~supfam		Grouping of sequence families into superfamilies
	SYSTERS		http://systers.molgen.mpg.de/		Classification of protein sequences into disjoint clusters with annotations from various other resources
	TMPDB		http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB		Experimentally-characterized transmembrane topologies
Proteome Resources
	AAindex		http://www.genome.ad.jp/dbget/		Physicochemical properties of peptides
	GELBANK		http://gelbank.anl.gov		2D-gel electrophoresis patterns from completed genomes
	PEP: Predictions for Entire Proteomes		http://cubic.bioc.columbia.edu/pep/		Signalling domain sequences
	Proteome Analysis Database		http://www.ebi.ac.uk/proteome/		Online application of interpro and clustr for the functional classification of proteins in whole genomes
	REBASE		http://rebase.neb.com/rebase/rebase.html		Restriction enzymes and associated methylases
	SWISS-2DPAGE		http://www.expasy.ch/ch2d/		Annotated two-dimensional polyacrylamide gel electrophoresis database
RNA Sequences
	5S Ribosomal RNA Database		http://biobases.ibch.poznan.pl/5SData		5S rRNA sequences
	16S and 23S Ribosomal RNA Mutation Database		http://www.fandm.edu/Departments/ Biology/Databases/RNA.html		16S and 23S rRNA mutations
	ACTIVITY		http://wwwmgs.bionet.nsc.ru/ mgs/systems/activity/		Functional DNA/RNA site activity
	ARED		http://rc.kfshrc.edu.sa/ared/		AU-rich element-containing mRNAs
	Database for mobile group II introns		http://www.fp.ucalgary.ca/group2introns		Database for mobile group II introns
	Collection of mRNA-like Noncoding RNAs		http://biobases.ibch.poznan.pl/ncRNA/		Non-protein-coding RNA transcripts
	European Ribosomal RNA Database		http://oberon.rug.ac.be:8080/ rRNA/index.html		Alignment of ribosomal RNA sequences with secondary structure information
	Guide RNA Database		http://biosun.bio.tu-darmstadt.de/ goringer/gRNA/gRNA.html		Guide RNA sequences
	HyPaLib		http://bibiserv.techfak. uni-bielefeld.de/HyPa/		Structural elements characteristic for classes of RNA
	Intronerator		http://www.cse.ucsc.edu/ ~kent/intronerator/		RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
	IRESdb		http://ifr31w3.toulouse.inserm.fr/ IRESdatabase/		Internal ribosome entry sites
	NCIR		http://prion.bchs.uh.edu/bp_type/		Non-standard base-base interactions in known RNA structures
	Noncoding regulatory RNAs Database		http://biobases.ibch.poznan.pl/ncRNA		Noncoding RNAs with regulatory functions
	Noncoding regulatory RNAs database		http://www.prl.msu.edu/PLANTncRNAs/		Plant non-protein coding RNAs with relevant gene expression information
	Plant snoRNA DB		http://bioinf.scri.sari.ac.uk/ cgi-bin/plant_snorna/home		snoRNA genes in plant species
	PLMItRNA		http://bighost.area.ba.cnr.it/PLMItRNA/		Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
	Pseudobase		http://wwwbio.leidenuniv.nl/ ~Batenburg/PKB.html		Information on RNA pseudoknots
	Rfam		http://www.sanger.ac.uk/Software/Rfam/		Non-coding RNA families
	Ribosomal Database Project (RDP II)		http://rdb.cme.msu.edu		rRNA sequence data, analysis tools, alignments and phylogenies
	RISCC		http://ulises.umh.es/RISSC		Ribosomal 16S-23S RNA gene spacer regions
	RNA Modification Database		http://medlib.med.utah.edu/RNAmods/		Naturally modified nucleosides in RNA
	SELEXdb		http://wwwmgs.bionet.nsc.ru/ mgs/systems/selex/		Selected DNA/RNA functional site sequences
	Small RNA Database		http://mbcr.bcm.tmc.edu/smallRNA		Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
	SRPDB		http://psyche.uthct.edu/dbs/ SRPDB/SRPDB.html		Signal recognition particle RNA, SRP protein and SRP receptor sequences and alignments
	Subviral RNA database		http://132.210.163.235/subviral/home.cgi		Database of viroids and viroid-like RNAs
	tmRDB		http://psyche.uthct.edu/dbs/ tmRDB/tmRDB.html		tmRNA (10Sa RNA) sequences and alignments
	The tmRNA Website		http://www.indiana.edu/~tmrna		tmRNA sequences, foldings, and alignments
	tRNA Sequences		http://www.uni-bayreuth.de/ departments/biochemie/trna/		tRNA and tRNA gene sequences
	UTRdb/UTRsite		http://bighost.area.ba.cnr.it/srs6/		5' and 3' UTRs of eukaryotic mRNAs and relevant functional patterns
	Yeast snoRNA Database		http://www.bio.umass.edu/biochem/ rna-sequence/Yeast_snoRNA_Database/ snoRNA_DataBase.html		Yeast small nucleolar RNAs
Retrieval Systems and Database Structure
	TESS		http://www.cbil.upenn.edu/tess		Transcription element search system
	Virgil		http://www.infobiogen.fr/services/virgil		Database interconnectivity
Structure
	ASTRAL		http://astral.stanford.edu/		Sequences of domains of known structure, selected subsets, and sequence-structure correspondences
	BioImage		http://www.bioimage.org		Searchable database of multidimensional biological images
	BioMagResBank		http://www.bmrb.wisc.edu/		NMR spectroscopic data from proteins, peptides, and nucleic acids
	CADB		http://144.16.71.148		Conformation angles of protein structures, with associated crystallographic data
	CATH		http://www.biochem.ucl.ac.uk/bsm/cath/		Hierarchical classification of protein domain structures
	CE		http://cl.sdsc.edu/ce.html		Combinatorial Extension: A Resource to Compute and Review 3-D Protein Structure Alignments
	CKAAPs DB		http://ckaap.sdsc.edu		Structurally-similar proteins with dissimilar sequences
	CSD		http://www.ccdc.cam.ac.uk/ prods/csd/csd.html		Crystal structure information for organic and metal organic compounds
	Database of Macromolecular Movements		http://bioinfo.mbb.yale.edu/MolMovDB/		Descriptions of protein and macromolecular motions, including movies
	Decoys 'R' Us		http://dd.stanford.edu/		Computer-generated protein conformations based on sequence data
	DSDBASE		http://www.ncbs.res.in/%7Efaculty/ mini/dsdbase/dsdbase.html		Native and modeled disulfide bonds in proteins
	DSMM		http://projects.eml.org/mcm/database/dsmm		Database of simulated molecular motions
	E-MSD		http://www.ebi.ac.uk/msd		Collected data on macromolecular structures
	FAMSBASE		http://famsbase.bio.nagoya-u.ac.jp/ famsbase		Protein three-dimensional structural models
	Gene3D		http://www.biochem.ucl.ac.uk/bsm cath_new/Gene3D/		Precalculated structural assignments for genes within whole genomes
	GTOP		http://spock.genes.nig.ac.jp/ ~genome/gtop.html		Structures of small molecules (hetero-compounds)
	HIC-Up		http://xray.bmc.uu.se/hicup/		Structures of small molecules (hetero-compounds)
	HSSP		http://www.sander.ebi.ac.uk/hssp/		Structural families and alignments; structurally-conserved regions and domain architecture
	IMB Jena Image Library of Biological Macromolecules		http://www.imb-jena.de/IMAGE.html		Visualization and analysis of three-dimensional biopolymer structures
	ISSD		http://www.protein.bio.msu.su/issd/		Integrated sequence and structural information
	LPFC		http://www-smi.stanford.edu/ projects/helix/LPFC/		Library of protein family core structures
	MMDB		http://www.ncbi.nlm.nih.gov/Structure/		All experimentally-determined three-dimensional structures, linked to NCBI Entrez
	ModBase		http://guitar.rockefeller.edu/modbase		Annotated comparative protein structure models
	MolMovDB		http://MolMovDB.org		Database of macromolecular movements
	NDB		http://ndbserver.rutgers.edu/		Nucleic acid-containing structures
	NTDB		http://ntdb.chem.cuhk.edu.hk		Thermodynamic data for nucleic acids
	PALI		http://pauling.mbu.iisc.ernet.in/~pali		Phylogeny and alignment of homologous protein structures
	PASS2		http://ncbs.res.in/%7Efaculty/ mini/campass/pass.html		Structural motifs of protein superfamilies
	PDB		http://www.rcsb.org/pdb/		Structure data determined by X-ray crystallography and NMR
	PDB-REPRDB		http://www.cbrc.jp/papia/papia.html		Representative protein chains, based on PDB entries
	PDBsum		http://www.biochem.ucl.ac.uk/bsm/pdbsum		Summaries and analyses of PDB structures
	PRESAGE		http://presage.berkeley.edu/		Protein structures with experimental and predictive annotations
	ProTherm		http://www.rtc.riken.go.jp/ jouhou/protherm/protherm.html		Thermodynamic data for wild-type and mutant proteins
	PSSH		http://srs3d.ebi.ac.uk/		Alignment between protein sequences and tertiary structures
	RESID		http://www-nbrf.georgetown.edu/ pirwww/dbinfo/resid.html		Protein structure modifications
	RNABase		http://www.rnabase.org		RNA-containing structures from PDB and NDB
	SCOP		http://scop.mrc-lmb.cam.ac.uk/scop/		Familial and structural protein relationships
	SCOR		http://scor.lbl.gov		RNA structural relationships
	SLoop		http://www-cryst.bioc.cam.ac.uk/~sloop/		Classification of protein loops
	Structure-Superposition Database		http://ssd.rbvi.ucsf.edu		Pairwise superposition of TIM-barrel structures
	SUPERFAMILY		http://supfam.org		Assignments of proteins to structural superfamilies
	TOPS		http://www.tops.leeds.ac.uk/		Topology of protein structure
Transgenics
	Cre Transgenic Database		http://www.mshri.on.ca/nagy/		Cre transgenic mouse lines
	Transgenic/Targeted Mutation Database		http://tbase.jax.org/		Information on transgenic animals and targeted mutations
Micellaneous Biomedical Content
	BAliBASE		http://www-igbmc.u-strasbg.fr/ BioInfo/BAliBASE2/index.html		Benchmark database for comparison of multiple sequence alignments
	Cytokine Gene Polymorphism in Human Disease		http://bris.ac.uk/pathandmicro/ services/GAI/cytokine4.htm		Cytokine gene polymorphism literature database
	DBcat		http://www.infobiogen.fr/services/dbcat/		Catalog of databases
	GlycoSuiteDB		http://www.glycosuite.com		N- and O-linked glycan structures and biological source information
	HOX-PRO		http://www.iephb.nw.ru/labs/lab38/ spirov/hox_pro/hox-pro00.html		Clustering of homeobox genes
	Imprinted Genes and Parent-of-Origin Effects		http://www.otago.ac.nz/IGC		Imprinted genes and parent-of-origin effects in animals
	LocusLink/RefSeq		http://www.ncbi.nlm.nih.gov/LocusLink/		Curated sequence and descriptive information about genetic loci
	MPDB		http://www.biotech.ist.unige.it/ interlab/mpdb.html		Information on synthetic oligonucleotides proven useful as primers or probes
	NCBI Taxonomy Browser		http://www.ncbi.nlm.nih.gov/ Taxonomy/taxonomyhome.html		Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence
	PDBsum		http://srs.ebi.ac.uk/		Molecular Probe Database
	probeBase		http://www.microbial-ecology.net/ probebase/		rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information
	PubMed		http://www.ncbi.nlm.nih.gov/PubMed/		MEDLINE and Pre-MEDLINE citations
	RefSeq		http://www.ncbi.nih.gov/RefSeq/		Reference sequence standards for genomes, genes, transcripts and proteins
	RIDOM		http://www.ridom.de/		rRNA (16S and ITS) sequence-based identification of medical microorganisms
	SWEET-DB		http://www.dkfz-heidelberg.de/ spec2/sweetdb		Annotated carbohydrate structure and substance information
	The Pharmacogenomics and Pharmacogenetics Knowledge Base		http://www.pharmgkb.org		Variation in drug response based on human variation
	Tree of Life		http://tolweb.org/tree/phylogeny.html		Information on phylogeny and biodiversity
	Vectordb		http://life.nthu.edu.tw/ ~g854202/Vecdtb.html		Characterization and classification of nucleic acid vectors
	VirOligo		http://viroligo.okstate.edu		Virus-specific oligonucleotides for PCR and hybridization
Original compilation by A. D. Baxevanis (Nucl. Acids Res. 29 [2001] 1-10) - updated June 2003

Impress  /  23-6-2003  /  R. Bergmann  /  http://www.biologie.uni-hamburg.de/molinkp.htm	search