Databases
| Molecular Biology DB collection Classified by | |||
| - Major sequence repositorie - Comparative Genomic - Gene Expression - Magest - Gene identification and structure - Genetic Maps - Genomic DB - Intermolecular interaction - Metabolic pathways and cellular regulation - Mutation DB |
- Pathology - Protein DB - Protein sequence motifs - Proteome resources - Retrieval systems and DB structure - RNA sequences - Structure - Transgenics - Varied biomedical content - Additional DB |
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| Major sequence repositorie + GenBank All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration + EMBL Nucleotide Sequence Database All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration + DNA Data Bank of Japan (DDBJ) All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration + Genome Sequence Database (GSDB) All known nucleotide and protein sequences + TIGR Gene Indices : Non-redundant, gene-oriented clusters + UniGene : Non-redundant, gene-oriented clusters |
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Comparative Genomics |
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| Gene Expression + ASDB : Protein products and expression patterns of alternatively-spliced genes + Axeldb : Gene expression in Xenopus + BodyMap : Human and mouse gene expression data + EpoDB: Genes expressed in vertebrate RBC + FlyView : Drosophila development and genetics + Gene Expression Database (GXD) : Mouse gene expression and genomics + Kidney Development Database : Kidney development and gene expression + MAGEST : Ascidian (Halocynthia roretzi) gene expression patterns + Mouse Atlas and Gene Expression Database : Spatially-mapped gene expression data + PEDB : Normal and aberrant prostate gene expression + Tooth Development Database : Gene expression in dental tissue + TRIPLES : TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces |
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| Gene Identification and Structure + Ares Lab Intron Site : Yeast spliceosomal introns + COMPEL : Composite regulatory elements + CUTG : Codon usage tables + EID : Protein-coding, intron-containing genes + EPD : Eukaryotic POL II promoters + ExInt : Exonintron structure of eukaryotic genes + IDB/IEDB : Intron sequence and evolution + PLACE : Plant cis-acting regulatory elements + PlantCARE : Plant cis-acting regulatory elements + TransTerm : Codon usage, start and stop signals + TRRD : Regulatory regions of eukaryotic genes + YIDB : Yeast nuclear and mitochondrial intron sequences |
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| Genetic Maps + GeneMap '99 : International Radiation Mapping Consortium human gene map + G3-RH : Stanford G3 and TNG radiation hybrid maps + GB4-RH : Genebridge4 (GB4) human radiation hybrid maps + GDB : Human genes and genomic maps + DRESH : Human cDNA clones homologous to Drosophila mutant genes + GenAtlas : Human genes, markers and phenotypes + HuGeMap : Human genome genetic and physical map data + IXDB : Physical maps of human chromosome X + Radiation Hybrid Database : Radiation hybrid map data |
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| Genomic Databases + ACeDB Caenorhabditis elegans, Schizosaccharomyces pombe and human sequences and genomic information + FlyBase : Drosophila sequences and genomic information + Mouse Genome Database (MGD) : Mouse genetics and genomics + Saccharomyces Genome Database (SGD) : Saccharomyces cerevisiae genome + AMmtDB : Metazoan mitochondrial DNA sequences + Arabidopsis Database (AtDB) : Arabidopsis thaliana genome + CropNet : Genome mapping in crop plants + CyanoBase : Synechocystis sp. genome + EcoGene : Escherichia coli K-12 sequences + EMGlib : Completely sequenced bacterial genomes and the yeast genome + GOBASE : Organelle genome database + HIV Sequence Database : HIV RNA sequences + Human BAC Ends Database : Non-redundant human BAC end sequences + INE : Rice genetic and physical maps and sequence data + Mendel Database Database of plant EST and STS sequences annotated with gene family information + MitBASE : Mitochondrial genomes, intra-species variants, and mutants + MitoDat : Mitochondrial proteins (predominantly human) + MITOMAP : Human mitochondrial genome + MITONUC/MITOALN : Nuclear genes coding for mitochondrial proteins + MITOP : Mitochondrial proteins, genes and diseases + Munich Information Center for Protein Sequences (MIPS) : Protein and genomic sequences + NRSub : Bacillus subtilis genome + Phytophthora Genome Initiative Database : Oomycete sequences and genetic maps + RsGDB : Rhodobacter sphaeroides genome + TIGR Microbial Database : ¢®¢®Microbial genomes and chromosomes + ZFIN¢®¢®¡Ì : ¡Ì¨Ï ¡Ì¨¬Zebrafish genetics and development; mutant and wild-type lines + ZmDB¢®¢®¡Ì : ¡Ì¨Ï¡Ì¨¬Maize genome database |
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| Intermolecular Interactions + Database of Ribosomal Crosslinks (DRC) : Ribosomal crosslinking data + DIP : Catalog of proteinprotein interactions + DPInteract : Binding sites for Escherichia coli DNA-binding proteins |
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| Metabolic Pathways and Cellular
Regulation + Kyoto Encyclopedia of Genes and Genomes (KEGG) :Metabolic and regulatory pathways + EcoCyc Escherichia coli K-12 genome, gene products and metabolic pathways + ENZYME : Enzyme nomenclature + EpoDB : Genes expressed during human erythropoiesis + FlyNets : Drosophila melanogaster molecular interactions + Klotho : Collection and categorization of biological compounds + LIGAND : Enzymatic ligands, substrates and reactions + RegulonDB : Escherichia coli pathways and regulation + UM-BBD Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds + WIT2 : Integrated system for functional curation and development of metabolic models |
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| Mutation Databases + Online Mendelian Inheritance in Man (OMIM) Catalog of human genetic and genomic disorders + ALFRED : Allele frequencies and DNA polymorphisms + Androgen Receptor Gene Mutations Database : Mutations in the androgen receptor gene + Asthma and Allergy Database Genetics of allergy and asthma, including linkage studies and mutation data + Asthma Gene Database :Linkage and mutation studies on the genetics of asthma and allergy + Atlas of Genetics and Cytogenetics in Oncology and Hematology Chromosomal abnormalities in cancer + BTKbase : Mutation registry for X-linked agammaglobulinemia + Cytokine Gene Polymorphism Database Cytokine gene polymorphisms, in vitro expression and disease-association studies + Database of Germline p53 Mutations : Mutations in human tumor and cell line p53 gene + dbSNP : Single nucleotidepolymorphisms + GRAP Mutant Databases : Mutants of family A G-Protein Coupled Receptors (GRAP) + Haemophilia B Mutation Database Point mutations, short additions and deletions in the Factor IX gene + HAMSTeRS : Hemophilia A mutation database + HGBASE : Intragenic sequence polymorphisms + HIV-RT : HIV reverse transcriptase and protease sequence variation + Human Gene Mutation Database (HMGD) Known (published) gene lesions responsible for human inherited disease + Human PAX2 Allelic Variant Database : Mutations in human PAX2 gene + Human PAX6 Allelic Variant Database : Mutations in human PAX6 gene + Human Type I and Type III Collagen Mutation Database Human type I and type III collagen gene mutations + HvrBase : Primate mtDNA control region sequences + iARC p53 Database Missense mutations and small deletions in human p53 reported in peer-reviewed literature. + KinMutBase : Disease-causing protein kinase mutations + KMDB : Mutations in human eye disease genes + MmtDB : Mutations and polymorphisms in metazoan mitochondrial DNA sequences + Mutation Spectra Database : Mutations in viral, bacterial, yeast and mammalian genes + NCL Mutations : Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes + p53 Databases Human p53 and hprt mutations; transgenic lacZ and transgenic/bacterial lacI mutations + PAHdb : Mutations at the phenylalanine hydroxylase locus + PMD : Compilation of protein mutant data + RB1 Gene Mutation Database : Mutations in the human retinoblastoma (RB1) gene + Ribosomal RNA Mutational Database : 16S and 23S ribosomal RNA mutation database + SV40 Large T-Antigen Mutant Database : Mutations in SV40 large tumor antigen gene |
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| Pathology + FIMM Functional molecular immunology data (diseases, antigens, peptides and HLA binding sites + Mouse Tumor Biology Database (MTB) Mouse tumor names, classification, incidence, pathology, genetic factors + PEDB : Sequences from prostate tissue and cell type-specific cDNA libraries |
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| Protein Databases
+ AARSDB : Aminoacyl-tRNA synthetase sequences + DAtA : Annotated coding sequences from Arabidopsis + DExH/D Family Database : DEAD-box, DEAH-box and DExH-box proteins + Endogenous GPCR List : G protein-coupled receptors; expression in cell lines + ESTHER : Esterases and -hydrolase enzymes and relatives + FUNPEP : Low-complexity or compositionally-biased protein sequences + GenProtEC : Escherichia coli genes, gene products and homologs + GPCRDB : G protein-coupled receptors + GPMdb : Global Proteome Machine Organization Proteomics Database and Open Source Software www.thegpm.org + Histone Sequence Database : Histone and histone-fold sequences and structures + HIV Molecular Immunology Database : HIV epitopes + Homeobox Page : Information relevant to homeobox proteins, classification and evolution + Homeodomain Resource Homeodomain sequences, structures, and related genetic and genomic information + HUGE : Large (>50 kDa) human proteins and cDNA sequences + IMGT : Immunoglobulin, T cell receptor and MHC sequences + InBase : Intervening protein sequences (inteins) and motifs + Kabat Database : Sequences of proteins of immunological interest + LGIC : Ligand-gated ion channel sequences, alignments and phylogeny + Membrane Protein Database Membrane protein sequences, transmembrane regions and structures + MEROPS : Peptidase sequences and structures + MHCPEP : MHC-binding peptides + NRR : Steroid and thyroid hormone receptor superfamily + Olfactory Receptor Database : Sequences for olfactory receptor-like molecules + ooTFD : Transcription factors and gene expression + Peptaibol : Peptaibol (antibiotic peptide) sequences + PhosphoBase : Protein phosphorylation sites + PKR Protein kinase sequences, enzymology, genetics, and molecular and structural properties + PPMdb : Arabidopsis plasma membrane protein sequence and expression data + Prolysis : Proteases and natural and synthetic protease inhibitors + PROMISE : Prosthetic centers and metal ions in protein active sites + Protein Information Resource (PIR) : Non-redundant protein sequence database + Receptor Database (RDP) : Receptor protein sequences + Ribonuclease P Database : RNase P sequences, alignments and structures + SENTRA : Sensory signal transduction proteins + SWISS-PROT/TrEMBL : Curated protein sequences + TRANSFAC : Transcription factors and binding sites + Wnt Database : Wnt proteins and phenotypes |
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| Protein Sequence Motifs + BLOCKS : Protein sequence motifs and alignments + PROSITE : Biologically-significant protein patterns and profiles + Pfam : Multiple sequence alignments and hidden Markov models of common protein domains + O-GLYCBASE : Glycoproteins and O-linked glycosylation sites + PIR-ALN : Protein sequence alignments + PRINTS : Protein squence motifs and signatures + ProClass : Families defined by PROSITE patterns and PIR superfamilies + ProDom : Protein domain families + ProtoMap : Automated hierarchical classification of SWISS-PROT proteins + SBASE : Annotated protein domain sequences + SMART : ¡Ì¨¬ Signalling domain sequences + SYSTERS : ¡Ì¨¬Protein clusters |
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| Proteome Resources + AAindex : Physicochemical properties of peptides + REBASE : Restriction enzymes and associated methylases + SWISS-2DPAGE : 2D-PAGE images and reference maps + Yeast Proteome Database (YPD) : Saccharomyces cerevisiae proteome |
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| Retrieval Systems and Database
Structure + KEYnet : Keywords extracted from EMBL and GenBank + Virgil : Database interconnectivity |
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| RNA Sequences + 5S Ribosomal RNA Databank : 5S rRNA sequences + ACTIVITY : Functional DNA/RNA site sequences + Collection of mRNA-like non-coding RNAs : ¢®¢®Non-protein-coding RNA transcripts + Database on the Structure of Large Subunit Ribosomal RNA Alignment of large subunit ribosomal RNA sequences + Database on the Structure of Small Subunit Ribosomal RNA Alignment of small subunit ribosomal RNA sequences + Guide RNA Database : Guide RNA sequences + Intronerator : RNA splicing and gene structure in Caenorhabditis elegans + Non-canonical Base Pair Database : RNA structures containing rare base pairs + PLMItRNA : Plant mitochondrial tRNAs and tRNA genes + Pseudobase : Information on RNA pseudoknots + Ribosomal Database Project (RDP) : rRNA sequences, alignments, and phylogenies + RNA Modification Database : Naturally modified nucleosides in RNA + SELEX_DB : Selected DNA/RNA functional site sequences + Small RNA Database : Direct sequencing of small RNA sequences + SRPDB : Signal recognition particle RNA, protein, and receptor sequences + tmRDB : tmRNA (10Sa RNA) sequences + tmRNA Website : tmRNA (10Sa RNA) sequences + tRNA Sequences : tRNA and tRNA gene sequences + UTRdb : 5' and 3' UTRs of eukaryotic mRNAs + Viroid and Viroid-Like RNA Database : Viroid and viroid-like RNA and vHDV sequences + Yeast snoRNA Database ¢®¢® : Yeast small nucleolar RNAs |
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| Structure + PDB : Structure data determined by X-ray crystallography and NMR + CATH : Hierarchical classification of protein domain structures + SCOP : Familial and structural protein relationships + ASTRAL : Analysis of protein structures and their sequences + BioImage : Searchable database of multi-dimensional biological images + BioMagResBank : NMR spectroscopic data from proteins, peptides and nucleic acids + CSD : Crystal structure information for organic and metal organic compounds. + Database of Macromolecular Movements Descriptions of protein and macromolecular motions, including movies + Decoys 'R' Us : Computer-generated protein conformations based on sequence data + HIC-Up : Structures of small molecules ('hetero-compounds') + HSSP Structural families and alignments; structurally-conserved regions and domain architecture + IMB Jena Image Library Visualization and analysis of three-dimensional biopolymer structures + ISSD : Integrated sequence and structural information + LPFC : Library of protein family core structures + MMDB : All three-dimensional structures, linked to NCBI Entrez system + MODBASE ¢®¢® : Comparative protein structure models + NDB : Nucleic acid-containing structures + PDB-REPRDB : Representative protein chains, based on PDB entries + PRESAGE : Protein structures with experimental and predictive annotations + Protein Motions Database : Motions of protein loops, domains and subunits + ProTherm : Thermodynamic data for wild-type and mutant proteins + RESID : Protein structure modifications |
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| Transgenics + Cre Transgenic Database : Cre transgenic mouse lines + Transgenic/Targeted Mutation Database Information on transgenic animals and targeted mutations |
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| Varied Biomedical Content + CarbBank : Complex carbohydrate/polysaccharide sequences + DBcat : Catalog of databases + DrugDB : Pharmacologically-active compounds; generic and trade names + HOX-PRO : Clustering of homeobox genes + LocusLink/RefSeq : Curated sequence and descriptive information about genetic loci + Molecular Probe Database : Synthetic oligonucleotides, probes and PCR primers + MPDB : Information on synthetic oligonucleotides + NCBI Taxonomy Browser Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence + PubMed : MEDLINE and Pre-MEDLINE citations + Tree of Life : Information on phylogeny and biodiversity + Vectordb : Characterization and classification of nucleic acid vectors |
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| Additional Database + FastA : based compilation of higher plant mitochondrial tRNA genes + aCHEdb the database system for ESTHER, the [alpha]/[beta] fold family of protein and the Cholinesterase gene server + Ad5 E1A database mutations affecting the early region 1A (E1A) proteins of human adenovirus type 5 + APC gene database of germline and somatic mutations in human tumors and cell lines + AtDB : Arabidopsis thaliana Database + Compilation of tRNA sequences and sequences of tRNA gene + Dali Domain Dictionary + DRC : Database of Ribosomal Cross links + ECD : Escherichia coli database + germline p53 mutations in cancer-prone families + GIF-DB, FlyNets two WWW databases describing molecular (protein-DNA, protein-RNA and protein-protein) interactions occuring in the fly Drosophila melanogaster + GLYCBASE : database of O-glycosylated proteins + Human Collagen Mutation Database + Human Gene Mutation DB + LDLRDatabase : Mutations in the LDL receptor gene (LDLR) + Marfandatabase is a software that contains routines for the analysis of mutations identified in the FBN1 gene that encodes fibrillin-1 + MGD : Mouse Genome Database + MIPS : Munich Information Center for Protein Sequences of the German + National Center for Environment and Health (GSF) + mutations in the human WT1 gene + Neal's DNA Mutation Site Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents + Nuclear Receptor Resource + RHdb : a public database for radiation hybrid data + SGD : Saccharomyces Genome + Database + structure of large ribosomal subunit RNA + structure of small ribosomal subunit RNA + SWISS-PROT + TRANSFAC, TRRD and COMPEL : Databases on transcriptional regulation + U-insertion/deletion Edited Sequence Database + UMBER provides facilities for interrogating the PRINTS fingerprint database and the OWL composite sequence database + Universal Mutaion DB : software and databases for mutations in human genes + 16SMDBexp and 23SMDBexp : 16S and 23S Ribosomal RNA Mutation Databases |
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