DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
|The Bioinformatics Educational Resource" info|
This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.
|5S Ribosomal RNA|
5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA structure and RNA-protein interactions.
|A C. elegans DataBase|
AceDB is a genome database designed specifically for handling bioinformatic data flexibly.
AceView offers an integrated view of the human and nematode genes as reconstructed by alignment of all publicly available mRNAs and ESTs on the genome sequence.
|A CLAssification of genetic Mobile Elements|
Prokaryotic Mobile Genetic Elements (MGE's) are central players in mobilizing genes, whether within a given genome (intra-cellular mobility) or between bacterial cells (inter-cellular mobility). Traditionally, MGE's have been classified as either bacteriophages, plasmids or transposons. This classification becomes more and more obsolete as many chimerical elements are identified, which display strong similarities with elements of different families.
|X-linked Adrenoleukodystrophy Database|
Dtabase about adrenoleukodystrophy, a progressive, genetic disorder, which affects the adrenal glands and the white matter of the nervous system.
|Alternative Exon Database|
AEDB is a manual generated database for human alternative exons and their properties - the data is gathered from literature where these exons have been experimentally verified.
|The Arab Genetic Disease Database" info|
Database about of genetic disorders found in Arab populations.
|ALPORT Syndrome and COL4A5|
Alport Syndrome is a progressive renal disease with cochlear and ocular involvement. The most common form (~80%) is inherited in an X-linked pattern. X-linked Alport Syndrome (OMIM #301050) is caused by mutations in the type IV collagen alpha chain 5 (COL4A5).
The aim of this database is to record all known variants in the COL4A5 gene and their clinical significance. The GenBank sequence NC_000023.9 is used as the reference sequence. The Human Genome Variation Society nomenclature has been used to describe COL4A5 mutations, as well as original nomenclature described by Zhou et al (1994), which includes 202 nucleotides of 5' UTR.
ARUP offers full gene sequencing analysis (test 0051786) for classic X-linked Alport syndrome (80% of mutations) and targeted testing for p.C1564S (c.4692G>A), p.L1649R (c.4946T>G), p.R1677Q (c.5232G>A) mutations for adult type Alport syndrome (test 0051710).
AltExtron is a computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns. The alternative events have been delineated and annotated with various characterizations.
|Alternative Splicing Database (AltSplice)|
AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations.
This list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules.
|Androgen Receptor Database|
Constitutional mutations in the androgen receptor gene (AR) impair androgen - dependent male sexual differentiation to various degrees. Somatic mutations in the AR have been found in metastatic prostate cancer. Severe constitutional androgen insensitivity (AI) yields an external female phenotype. Partial constitutional AI yields a range of external genital phenotypes
that vary from near - normal female to normal or near - normal male, with or without gynecomastia and other relatively "mild" signs of undervirilization. Some have suggested that clinical severity of AI be divided into three degrees: complete, partial, (when there is appreciable external genital ambiguity) and mild (for the least severe forms). Others have graded severity into seven degrees . The current version of the AR mutation database retains the complete / partial bifurcation of the original database, but provides additional information on the external genitalia and on sex - of - rearing. When external genital ambiguity is appreciable, the sex - of -rearing implies that the external genitalia were predominately male or female. Because different clinical degrees of AI are sometimes seen within families or between those with the same mutation, the new version of the database has an entry for family history.
|Pristionchus pacificus - Database" info|
Database about the nematode Pristionchus pacificus, created by the University Tuebingen, Germany.
Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms. These novel molecules have many potential uses in medicine and technology.
|Human AU-rich Element-Containing mRNA Database" info|
The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenuous agents such as microbes, inflammatory and environmental stimuli.
|Gene Regulation by Mammalian micro-RNAs|
MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis. By far the most important model systems in cancer research are mammalian organisms. Argonaute compiles comprehensive information on mammalian miRNAs, their origin and regulated target genes in an exhaustive database.
|Mutation Database - Autosomal Recessive Polycystic Kidney Disease (ARPKD / PKHD1)" info|
Autosomal Recessive Polycystic Kidney Disease (ARPKD) or Polycystic Kidney and Hepatic Disease 1 (PKHD1) is an important cause of childhood renal- and liver-related morbidity and mortality with a proposed incidence of 1:20,000 - 1:40,000 live births.
ArrayExpress is a public database of gene expression experiments. These experiments consist of multiple parts (or objects), in order to simplify querying we have provided a query interface which allows you to retrieve the most useful information relating to each experiment, the array(s) and the protocols(s) used.
|Alternative Spliced Isoforms|
After transcription of a gene, the resulting pre-mRNA is spliced before exiting the nucleus. Alternative splicing of a single pre-mRNA can give rise to different mRNA transcripts. Consequently, alternative splicing is an important mechanism for generating protein diversity from a single gene.
|Alternative Splicing Database Project|
Alternative splicing database at EBI; it includes three databases:
|Alternative Splicing Gallery" info|
ASG is a web-based splicing graph database that integrates transcript information from Ensembl, RefSeq, STACK, TIGR gene index, and UniGene, in order to explore and visualize gene structure and alternative splicing and to
provide an exhaustive transcript catalog.
|Alternatively Spliced Human genes by Exon Skipping|
Database about alternataive splicing.
|Atlas of Genetics" info|
The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases.
|The Autism Chromosome Rearrangement Database|
Database of chromosomal breakpoints and other genomic features related to autism, provided by the canadian Centre for Applied Genomics and The Hospital for Sick Children in Toronto.
|Xenopus laevis Database Focusing on Gene Expression" info|
Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The database was developed at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg.
Database about transcriptional regulators of AraC and TetR families.
Database about genes relevant to cardiovascular and pulmonary disease.
|Online Maps of Metabolic and Signaling Pathways|
Graphical display of pathways.
The BioCatalog is a software directory of general interest in molecular biology and genetics.
BioConductor is an open source and open development software project for the analysis and comprehension of genomic data.
|Database of Tetrahydrobiopterin Deficiencies - BIODEF / BIOMDEB|
International database of tetrahydrobiopterin deficiencies (BIODEF)
|Bipartite Pattern Discovery" info|
Bipad is a C++ program for predicting one-block or bipartite motifs/patterns shared by a set of nucleotide sequences. This tool, which is particularly useful for transcription factor binding site recognition, was developed by Chengpeng Bi and P.K. Rogan, Laboratory of Human Molecular Genetics, Children's Mercy Hospital and Clinics, 01 Gillham, Kansas City MO 64108
|Basic Local Alignment Search Tool" info|
Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and evolutionary information can be inferred from well designed queries and alignments. BLAST (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
|BLAT Search Genome" info|
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
BMRB is a repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids.
BodyMap is a database of expression information of human and mouse genes in various tissues or cell types and various timings.
BRAGI is an interactive protein modeling program. It was developed for the special
purpose to model unknown proteins from the structure of a known one. BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. One can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs. BRAGI includes also a set of programs and utility functions.
|Biomolecular Relations in Information Transmission and Expression|
BRITE is a database of binary relations for network computation and logical reasoning involving genes, proteins, and other biological molecules.
|Familial Hypertrophic Cardiomyopathy / DNA Mutation Database" info|
This database contains information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data.
CarpeDB is a epilepsy genetics database. It profiles some 400 genes linked to epilepsy in humans, mice, nematodes, and other organisms.
|Catalogue of Life|
The Catalogue of Life is indexing the world's known species.
|Genome Atlas Database" info|
Database of sequenced bacterial genomes.
|Consensus CDS (CCDS)|
The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality.
CellCircuits is a database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways.
|Cancer Genome Anatomy Project|
The Cancer Genome Anatomy Project (CGAP) is an interdisciplinary program established and administered by the National Cancer Institute (NCI) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
|Candida Genome Database|
The Candida Genome Database is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data.
CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
|Clusters of Orthologous Groups of Proteins" info|
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages.
|Database of Human Type I and Type III Collagen Mutations|
This database aims to record all published accounts of mutations in the genes encoding human collagen types I and III. Mutations of these collagen types result predominantly in osteogenesis imperfecta and Ehlers-Danlos syndrome type IV respectively.
|COmparative Regulatory Genomics" info|
CORG stands for COmparative Regulatory Genomics. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements.
|Catalogue Of Somatic Mutations In Cancer" info|
COSMIC (Catalogue of Somatic Mutations in Cancer; http://www.sanger.ac.uk/cosmic) is a comprehensive resource that aims to curate the world's literature on somatic mutations in known cancer genes. The catalog includes full and up-to-date curation of mutation data in over 60 well known point-mutated genes, together with novel gene fusion products expressed across genome rearrangement breakpoints, and all of the somatic mutation data from candidate gene screens at the UK's Cancer Genome Project.
|CpG Island Database|
UHN Microarray Centre's CpG Island Database. Here you will find all the information you need to get started with analysing your results from experiments performed on our HCGI 12K and HCGI 8.1K Microarray chip.
|CREB Target Gene Database" info|
In mammalian cells, an elevation in the cytosolic cAMP level stimulates the expression of many genes. All genes regulated by cAMP contain a cis-acting DNA sequence, called cAMP-response element (CRE), which binds the phosphorylated form of a transcription factor called CRE-binding (CREB) protein. Researchers can find out which genes the influential protein activates at the CREB Target Gene Database from Marc Montminy of the Salk Institute in La Jolla, California, and colleagues.
|Codon Usage Database|
Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site. CUTG was originally developed by Prof. Toshimichi Ikemura at Laboratory of Evolutionary Genetics, National Institute of Genetics. Codon Usage Database is developed and mainteined by Yasukazu Nakamura at The First Laboratory for Plant Gene Research, Kazusa DNA Research Institute.
|Cystic Fibrosis Mutation Database|
This database is devoted to the collection of mutations in the CFTR gene and is currently maintained by the laboratory of Lap-Chee Tsui on behalf of the international Cystic Fibrosis genetics research community. It was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers. The specific aim of the database is to provide CF researchers and other related professionals with up to date information about individual mutations in the CFTR gene.
|Transcription Factor Prediction Database" info|
DBD is a database of predicted transcription factors in genomes based on domain assignments from the SUPERFAMILY and PFAM hidden Markov model libraries. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families.
|Expressed Sequence Tags Database|
dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
|database of Genotypes and Phenotypes (dbGaP)|
The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.
|DBGET - Database Links" info|
DBGET is a simple database retrieval system for a diverse range of molecular biology databases.
|Genome Survey Sequences Database|
The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA).
The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC).
|Database for Preterm Birth" info|
The Database for Preterm Birth (dbPTB) is a web-based aggregation tool to organize the genes, genetic variations and pathways involved in preterm birth, dbPTB. We used semantic data mining to extract all published articles related to preterm birth. All articles were reviewed by a team of curators. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature.
dbQSNP is a database, that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones.
|Retrotransposon Insertion Polymorphisms in Humans Database|
dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs), in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. dbRIP contains all currently known Alu, L1, and SVA polymorphic insertion loci in the human genome.
|Single Nucleotide Polymorphism|
A key aspect of research in genetics is associating sequence variations with heritable phenotypes. The most common variations are single nucleotide polymorphisms (SNPs), which occur approximately once every 100 to 300 bases. Because SNPs are expected to facilitate large-scale association genetics studies, there has recently been great interest in SNP discovery and detection.
|Sequence Tagged Sites|
The STS division file contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites.
|Database of Transcriptional Start Sites|
Based on 400,225 and 580,209 human and mouse full-length cDNA sequences, DBTSS contains exact information of the genomic positions of the transcriptional start sites and the adjacent promoters for 8,793 and 6,875 human and mouse genes, respectively. Of these, 3,324 could be paired as mutually homologous genes between human and mouse and their promoters could be compared with each other.
dbZACH is a toxicogenomic information management system, built on a relational database and Java technology, used to store a variety of data generated or otherwise relevant to the Zacharewski lab. The goal of the project is to create a local data management product that is capable of serving the needs of small toxicology laboratories.
|DNA Data Bank of Japan" info|
DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG) with the endorsement of the Ministry of Education, Science, Sport and Culture. From the beginning, DDBJ has been functioning as one of the International DNA Databases, including EBI (European Bioinformatics Institute; responsible for the EMBL database) in Europe and NCBI (National Center for Biotechnology Information; responsible for GenBank database) in the USA as the two other members.
|Deafness Gene Mutation Database|
Gene mutation database about deafness, provided by the Harvard Medical School, Center for Hereditary Deafness.
|Database of Essential Genes" info|
Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell.
|Database Of Ribosomal Crosslinks|
In order to interpret the molecular basis of the translational process, it is essential to have a corresponding knowledge of the higher structure of the ribosome. A large amount of biochemical data about structure of the ribosome is available at present. Ribosomal cross-linking is one of the most important methods which allows us to get such data.
|Database of Simulated Molecular Motions" info|
The purpose of this database is to provide an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation. All of the movies are available through the internet.
|Macromolecular Structure Database" info|
The E-MSD macromolecular structure relational database is designed to be a single access point for protein and nucleic acid structures and related information.
EBI’s (European Bioinformatics Institute's) collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes.
|European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations" info|
ECARUCA is a database which collects and provides cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications.
ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration.
|Eukaryotic Gene Orthologs|
The Eukaryotic Gene Orthologs (EGO), is a database for orthologous genes in eukaryotes.
|Exon-Intron Database" info|
Datbase of protein-coding intron-containing genes.
|Edinburgh Mouse Atlas Project|
The Edinburgh Mouse Atlas consists of a digital atlas of mouse embryo development and spatially-mapped gene expression.
|EMBL Molecular Databases|
Molecular Databases, accessible by EMBL:
|EMBL Nucleotide Sequence Database" info|
The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource.
|Enhanced Microbial Genomes Library" info|
EMGLib is a database about the completely sequenced bacterial genomes and the yeast genome.
|ENCyclopedia Of DNA Elements" info|
The ENCODE project aims to discover functional elements in the human genome by intensively annotating 1% of the genome.
|Ensembl Genome Browser" info|
ENSEMBL is a joint project between EMBL-EBI and the Sanger Center to develop a system which automatically tracks all the sequenced pieces of human genome, attempts to assemble them into large single stretches and then analyse the assembled DNA to find genes and other features of interest to biologists and medical researchers.
Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
|Entrez Gene" info|
Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode.>br>
Entrez integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system.
|Entrez Genome" info|
The whole genomes of over 1000 viruses and over 100 microbes can be found in Entrez Genome. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles.
|Entrez Nucleotide Database" info|
The Nucleotide database contains sequence data from GenBank, EMBL, and DDBJ, the members of the tripartite, international collaboration of sequence databases. EMBL is the European Molecular Biology Laboratory (EMBL) at Hinxton Hall, UK; DDBJ is the DNA Database of Japan (DDBJ) in Mishima, Japan. Sequences are also incorporated from the Genome Sequence Data Base (GSDB), Santa Fe, NM. Patent sequences are incorporated through arrangements with the U.S. Patent and Trademark Office (USPTO), and via the collaborating international databases from other international patent offices.
|Entrez Structure" info|
The Structure database or Molecular Modeling DataBase (MMDB) contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from the Protein Data Bank (PDB). The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy.
|Endocrine Pancreas Consortium Database" info|
Genexpression database of the Endocrine Pancreas Consortium.
|The Eukaryotic Promoter Database|
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
|Epigenetics Product Database|
Database about laboratory products used in the epigenetic research field.
|EpiGenie - Databases & Tools|
Compilation of databases and tools on the field of epigenetics.
Pox genome database.
|Erythropoiesis Database" info|
The EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.
The database ist provided by the Computational Biology and Informatics Laboratory at the University of Pennsylvania.
|Exon - Intron Database of Eukaryotic Organisms|
The ExInt database incorporates information on exon-intron structure of eukaryotic genes. ExInt accumulates and describes following important characters of the eukaryotic genes: the phases and positions of introns and the exon size and positions of introns for all proteins in GenBank.
|Expert Protein Analysis System" info|
EXPASy (Expert Protein Analysis System) provides databases for the research on proteomics:
|ExPASy Proteomics Tools" info|
Tools for the analysis of the human proteom.
|Factor H Associated HUS - Mutation Database" info|
Database about the HUS (Haemolytic Uraemic Syndrome); this is a disease associated with microangiopathic haemolytic anemia, thrombocytopenia and acute renal failure. A subgroup of the syndrome is strongly associated with abnormalities within the complement regulator factor H gene.
|Functional Annotation of Mouse" info|
FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone.
|Factor H Associated HUS Mutation Database" info|
The Factor H Associated HUS Mutation Database is a database of mutations within the human complement Factor H protein that are associated with Haemolytic Uraemic Syndrome (HUS).
Flytrap is a database of transposable element insertions in Drosophila melanogaster.
|Drosophila Image Database" info|
FlyView is an image database for Drosophila development and genetics, particularly for gene-expression patterns.
|Malaria Full-Length cDNA Database (Plasmodium falciparum)|
Full Malria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum.
Fungal database, provided by
|The Human Ageing Genes Database" info|
GenAge ia a database of genes related to human ageing.
GenBank is a database of nucleotide sequences from >130,000 organisms. Records that are annotated with coding region (CDS) features also include amino acid translations. GenBank belongs to an international collaboration of sequence databases (described below), which also includes EMBL and DDBJ.
|Gene Cards" info|
GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
|Gene Connection for the Heart|
This database is a repository of the genetic variations identified and published in the field of inherited arrhythmogenic diseases and cardiac ion channels.
Gene3D is a database of annotated complete genomes.
|Microarray Gene Annotation (GeneAnnot)" info|
Revised and improved annotation of Affymetrix human gene probe sets.
|GeneLink: A Database to Facilitate Genetic Studies of Complex Traits" info|
GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data.
|Gene Location" info|
GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, Genome Database, and mapping resources. GeneLoc is presented by the Weizmann Institute of Science, Rehovot, Israel
GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers:
GenePaint is a digital atlas of gene expression patterns in the mouse.
Genes and Disease is a collection of articles that discuss genes and the diseases that they cause.
GeneSeeker is a database for the identification of genes underlying human genetic disorders. This requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes.
By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making.
|Genetic Association Database" info|
The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The aim of this database is to identify medically relevant polymorphism from the large volume of polymorphism and mutational data.
|The Genetic Codes|
Database about deviations from the standard genetic code in various organisms and organelles. Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A.
|GENETRAP / IGTC|
Gene trapping is a high-throughput approach that is used to introduce insertional mutations across the genome in mouse embryonic stem (ES) cells. In addition to generating standard loss-of-function alleles, newer gene trap vectors offer a variety of post-insertional modification strategies for the generation of other experimental alleles.
The International Gene Trap Consortium (IGTC) represents all publicly available gene trap cell lines, which are available on a non-collaborative basis for nominal handling fees. Researchers can search and browse the IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways.
|Genome Reviews" info|
The goal of the Genome Reviews project is to provide an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes.
|Genomes Server at the EBI|
The first completed genomes from viruses, phages and organelles were deposited into the EMBL Database in the early 1980's. Since then, molecular biology's shift to obtain the complete sequences of as many genomes as possible combined with major developments in sequencing technology resulted in hundreds of complete genome sequences being added to the database, including Archaea, Bacteria and Eukaryota. These web pages give access to a large number of complete genomes.
|Mycobacterium tuberculosis Database" info|
GenoMycDB was designed for large-scale comparative analysis, offering a variety of searching/retrieving methods. The selection of aligned pairs with specific attributes can be done based on one or multiple alignment parameters (section Filtering Options, sub-section HSP) – raw score (Score); bit score (Bits); fraction of identical positions for a given HSP (Identity%).
|Gene Expression Omnibus" info|
The Gene Expression Omnibus is a high-throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval. GEO became operational in July 2000.
GermOnline is a database that provides access to microarray expression data from experiments relevant for the mitotic and meiotic cell cycle as well as gametogenesis in yeast and higher eukaryotes. In addition to that, GermOnline integrates knowledge about genes important for sexual reproduction.
|Genome Information Broker" info|
DDBJ’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes.
|Globin Gene Server|
This site provides data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.
|Glyco-related Databases and Development of Bioinformatic tools for Glycobiology and Glycomics|
Compilation of databases about glycosylation, made by the DKFZ (German Cancer Research Center), Heidelberg.
|Gene Ontology Consortium Database" info|
The goal of the Gene OntologyTM (GO) Consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.
|Gene Ontology Annotation (GOA)" info|
The Gene Ontology Annotation (GOA) database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO).
|The Organelle Genome Database" info|
GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.
|Genomes OnLine Database" info|
Database of completed and ongoing genome projects.
|Genomics of Lipid-associated Disorders Database|
The GOLD.db was developed to address the need to integrate disparate information on the function and properties of genes and their protein products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders including non-insulin dependent diabetes, various hyperlipidemias, high blood pressure and atherosclerosis.
|Genetic Science Learning Center|
The Genetic Science Learning Center is an excellent tool for Helping people understand how genetics affects their lives and society.
|Genome Wide Association Database|
The genome wide association database (GWAS DB) is a repository system and has been constructed to achieve permanent data management and information sharing of genome wide association data. GWAS-DB contains experimental frequency data such as allele frequencies and genotype frequencies, and statistical genetics analysis results such as allelic model, dominant model, recessive model, and additive model and provides graphic viewer to search disease related SNP candidates.
|Mouse Gene Expression Database|
Gene expression database from the mouse.
|H-Invitational Database (H-InvDB)" info|
H-Invitational Database (H-InvDB) is a human gene database, with integrative annotation of 41,118 full-length cDNA clones currently available from six high throughput cDNA sequencing projects. This database represents 21,037 cDNA clusters describing their gene structures, functions, novel alternative splicing isoforms, non-coding functional RNAs, functional domains, sub-cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases, gene expression profiling, and comparative results with mouse full-length cDNAs in the context of molecular evolution.
|Haemophilia A Mutation Database|
The Database covers the following three main classes of mutant:
Point Mutations, Insertions, Deletions
|Haemophilia B Mutation Database|
A database of point mutations and short additions and deletions in the factor IX gene.
|Human Ageing Genomic Resources" info|
The Human Ageing Genomic Resources (HAGR) are a collection of databases and tools designed to help researchers understand the genetics of human ageing. A major resource in HAGR is the core gene database GenAge, a database of genes related to human ageing. Featuring over 2,000 species, AnAge provides a basis for the comparative biology of ageing.
|International HapMap Project" info|
The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors.
|Database of Human Hemoglobin Variants and Thalassemias" info|
Database about human hemoglobin variants and thalassemias.
|HCV Databases" info|
The Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The project comprises two databases:
|Hepatitis C - Database|
Database about hepatitis C.
Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome.
|Hematopoiesis Promoter Database (HemoPDB)" info|
The Hematopoiesis Promoter Database (HemoPDB) has been developed as a information resource focused on transcriptional regulation in hematopoiesis. HemoPDB is composed of integral, experimentally defined regulatory information, including TFs, cis-regulatory elements, their target gene promoters and corresponding annotations, with links to supporting published references. Accordingly, the database may be searched by Gene Symbol, GenBank Accession Number, UniGene ID, TF (binding site) Name and lineage or cell type within which a gene is expressed.
|Human Endogenous Retrovirus Database" info|
Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.
|Human Gene Mutation Database at the Intitute of Medical Genetics in Cardiff" info|
The Human Gene Mutation Database (HGMD) represents an attempt to collate known (published) gene lesions responsible for human inherited disease. This database, whilst originally established for the study of mutational mechanisms in human genes (Cooper and Krawczak 1993), has now acquired a much broader utility in that it embodies an up-to-date and comprehensive reference source to the spectrum of inherited human gene lesions. Thus, HGMD provides information of practical diagnostic importance to (i) researchers and diagnosticians in human molecular genetics, (ii) physicians interested in a particular inherited condition in a given patient or family, and (iii) genetic counsellors.
|Human Genome Variation Database|
The objective of HGVbase (the Human Genome Variation Database) is to provide an accurate, high utility and ultimately fully comprehensive catalog of normal human gene and genome variation, useful as a research tool to help define the genetic component of human phenotypic variation. All records are highly curated and annotated, ensuring maximal utility and data accuracy.
List of human genome variation databases. This list was compiled by Rania Horaitis at the Genomic Disorders Research Centre, Melbourne.
|Histone Database" info|
Eukaryotic chromatin is composed of DNA and protein components – core histones – that act to compactly pack the DNA into nucleosomes, the fundamental building-block of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone posttranslational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3, and H4), the linker histones (H1/H5), and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.
|HIV - Sequence Database|
The HIV Sequence Database focuses on five primary goals:
|HIV - Sequence Database|
The HIV Sequence Database focuses on five primary goals:
|HIV Structural Database and Chem-BLAST|
HIV Structural Reference Database and Chem-BLAST at NIST
Biotechnology Division, National Institute of Standards and Technology Gaithersburg, MD 20899 U.S.A.
|Human Metabolome Database" info|
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.
|Human Mitochondrial Protein Database (HMPDb)|
The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases.
|Homologous Processed Pseudogenes Database" info|
Hoppsigen is a nucleic database of homologous processed pseudogenes.
|Human Gene Expression Index (HuGE Index)" info|
Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
|Human Gene Nomenclature Database" info|
Database, produced by the HUGO Gene Nomenclature Committee, providing all the gene symbols.
|Human Genome Resources (ncbi)" info|
NCBI's Genome Browser.
|Encyclopedia of Human Genes and Metabolism|
HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome.
|Human siRNA Database|
The human siRNA database (HuSiDa) is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup and actual procedure of specific RNAi experiments in human cells.
The HvrBase is a tool for the analysis of human and primate mitochondrial DNA (mtDNA).
|X-linked SCID Mutation Database|
X-linked severe combined immunodeficiency (XSCID or X-SCID) is an immune disorder caused by mutations in the X-linked gene IL2RG, which encodes the common gamma chain (c) of the lymphocyte receptors for interleukin-2 (IL-2) and many other cytokines. A database of human XSCID mutations (IL2RGbase) has been assembled. Information on new mutations may be submitted online.
|Integrated Microbial Genomes (IMG)|
The Integrated Microbial Genomes (IMG) system provides a framework for the comparative analysis of the genomes sequenced by the Joint Genome Institute.
|ImMunoGene Tics Database" info|
The international ImMunoGeneTics information system (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire (LIGM; Universite Montpellier II and CNRS) at Montpellier, France
|Imgt / Primer - Database|
IMGT/PRIMER-DB was implemented by Julien Bertrand (LIGM, Montpellier, France) and Géraldine Folch (EUROGENTEC).
Informations about vertebrate immunoglobulin and T cell receptor genes.
|Repertory of Familial Mediterranean Fever and Hereditary Autoinflammatory Disorders Mutations" info|
Informations about the Familial Mediterranean Fever and hereditary autoinflammatory diseases.
Integr8 is a browser for information relating to completed genomes and proteomes, based on data contained in Genome Reviews and the UniProt proteome sets. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.
|The Interactive Fly|
Database about Drosophila genes and their roles in development.
|Interferon Stimulated Gene Database|
Database about genes induced by treatment with interferons.
|Alternative Splicing in Caenorhabditis elegans" info|
The Intronerator is a collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing.
|Intronless Genes in Eukaryotes" info|
Database about intronless genes.
|Internal Ribosome Entry Site Database|
Database about virally encoded IRESes and cellular mRNA encoded IRESes. It was developed by Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço and Stéphan Vagnerat The French Institute of Health and Medical Research.
|Internal Ribosome Entry Site Database|
The IRESite database contains information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
The IRESite database contains information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
|Influenza Sequence Database|
The Influenza Sequence Database is a curated database of nucleotide sequences. It is intended to provide the research community with easy sequence deposit and retrieval capabilities, together with tools tailored, in particular, to the analysis of hemagglutinin and neuraminidase sequences.
|IUPHAR Committee on Receptor Nomenclature and Drug Classification Database|
Receptor Nomenclature DAtabase by the International Union of Pharmacology (IUPHAR).
|Influenza Virus Database (IVDB)|
The Influenza Virus Database (IVDB) integrates information and creates an analysis platform for genetic, genomic, and phylogenetic studies of the virus.
|Transcription Factor Binding Profile Database (JASPAR)" info|
JASPAR is a collection of transcription factor DNA-binding preferences, modelled as position-specific weight matrices (PSSMs).
Jpo_prt - a library of patented protein sequences from the Japanese Patent Office in the public domain.
|Japanese SNP Database" info|
JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister’s Millennium Project. The aim of this undertaking is to identify and collate up to 150.000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence the coding sequence of the genes. The project has been carried out by a collaboration between the Human Genome Center (HGC) in the Institute of Medical Science (IMS) at the University of Tokyo and the Japan Science and Technology Corporation (JST).
|Kinetic Data of Bio-molecular Interactions Database" info|
KDBI provides experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature.
|Kyoto Encyclopedia of Genes and Genomes (KEGG)" info|
KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks in biological processes (PATHWAY database), the information about the universe of genes and proteins (GENES/SSDB/KO databases), and the information about the universe of chemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases).
|Kegg Expression Database|
KEGG/EXPRESSION is a database system for integrated analysis of gene expression profile data, together with KEGG pathway data and genome sequence data.
|Kidney Development Database|
The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development.
|Registry of Disease-causing Mutations in Protein Kinase Domains" info|
KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders.
|The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database|
Database about mutations and polymorphisms associated with Lafora progressive
|Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database" info|
Database about genes involved in the pathogenesis of Progressive Myoclonus Epilepsy (PME) of the Lafora type.
|Leukemia Gene Atlas|
The Leukemia Gene Atlas (LGA) is a public platform that supports the research and analysis of molecular data of leukemias. In addition to the molecular data the LGA stores the corresponding clinical and laboratory data. The LGA supports comprehensive queries of data, the visualization and analysis as well as download and upload. Currently, there are gene expression, methylation, sequencing data and genotypes of over 6000 samples in the LGA. To analyze data the user may choose between a set of tools: cluster analyses, statistical tests, data distribution plots and the Integrative Genomics Viewer (IGV).
|Lowe Syndrome Mutation Database|
Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. A database of mutations causing Lowe syndrome has been established. Information on new mutations may be submitted online.
|DeRisi Lab Malaria Transcriptome Database" info|
Database about the Malaria Transcriptome, provided by the University of California San Francisco.
|Multi-genome Analysis of Positions and Patterns of Elements of Regulation|
MAPPER is a platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes.
|Microbial Genome Database for Comparative Analysis|
MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly.
|Multiple Congenital Anomaly / Mental Retardation" info|
This database has been developed to facilitate the identification and differentiation of syndromic entities. Special attention is given to the type of information which, because of space the limitations of the printed form, is usually limited or completely omitted in the existing reference sources.
|Multiorganism Database of Metabolic Pathways and Enzymes" info|
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways from more than 300 different organisms.
|DNA Methylation Database" info|
Database of DNA methylation.
|Database for DNA Methylation and Environmental Epigenetic Effects" info|
The purpose of this database is to provide the scientific community with a resource to store DNA methylation data and to make these data readily available to the public. Futur development of the database will focus on environmental effects on DNA methylation. It attempts to store all data about DNA methylation in a common source. It can be searched in different ways, ranging from a simple browse mode to detailed queries for sequence-specific DNA methylation profiles and patterns, total methylation content data or environmental conditions that can influence the methylation state of DNA.
|Database of Human DNA Methylation and Cancer" info|
To study interplay of DNA methylation, gene expression and cancer, a database for human DNA Methylation and Cancer was developed. MethyCancer hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Furthermore, a powerful search tool is developed to provide user-friendly access to all the data and data connections. A graphical MethyView shows DNA methylation in context of genomics and genetics data facilitating the research in cancer to understand genetic and epigenetic mechanisms that make dramatic changes in gene expression of tumor cells.
|Mammalian Gene Collection|
The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. All MGC sequences are deposited in GenBank and the clones can be purchased from distributors of the IMAGE consortium.
|Mouse Genome Database" info|
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
|Marine Microbial Biodiversity Database" info|
Micro-Mar is a database for dynamic representation of marine microbial biodiversity.
Guide to microRNA and microRNA Databases.
microRNA.org is a resource for predicted microRNA targets and expression
provided by the Memorial Sloan-Kettering Cancer Center.
|Database of Mitochondrial Proteins" info|
MiGenes is a relational database of mitochondrial-related gene products. It includes major model organisms such as human, mouse, rat, fruit fly, worm, baker’s yeast and fission yeast.
|miRBase: microRNA data" info|
Database of microRNAs (small non-coding RNAs), provided by the Sanger Institute.
|Mitelman Database of Chromosome Aberrations in Cancer" info|
The information in the Mitelman Database of Chromosome Aberrations in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman, Bertil Johansson, and Fredrik Mertens.
|Mendelian Inheritance and the Mitochondrion|
This database is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although we are including proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria.
|Human Mitochondrial Genome Database" info|
MITOMAP is a compendium of polymorphisms and mutations of the human mitochondrial DNA.
|Mitochondrial Proteom Database" info|
Database about the mitochondrial proteom.
|Mobile Group II Introns|
Group II introns are a novel class of RNAs best known for their self-splicing reaction. Under certain in vitro conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of protein.
|Molecular Probe Data Base|
The Molecular Probe Data Base (MPDB) contains information on ca. 4.300 synthetic oligonucleotides with a sequence of up to 100 nucleotides.
|Human Mitochondrial Genome Database" info|
The Human Mitochondrial Genome Database (mtDB) provides a database of complete human mitochondrial genomes.
|Human Mitochondrial Genome Polymorphism Database|
The GiiB-JST mtSNP (mitochondrial single nucleotide polymorphism) database provides information related to the functional differences among mitochondrial SNPs. This web site is useful for identification of mtSNPs associated with age-related conditions such as longevity, Parkinson's disease, and Alzheimer's disease, as well as those related to energy metabolism such as obesity, thinness, and type-2 diabetes, or to atherosclerosis.
|Myc Cancer Gene" info|
Diese Website enthält Links zu folgenden Datenbanken:
|National Center for Biotechnology Information (NCBI / NLM / NIH)|
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
|The NCBI BioSystems Database|
The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.
|NCBI Map View" info|
Graphical view of chromosomes of different organisms, including homo sapiens.
|NCBI Map Viewer (Homo Sapiens Genome)" info|
The NCBI Map Viewer displays genome assemblies using sets of aligned chromosomal maps. A new Map Viewer home page organizes the available organisms by taxonomic group and provides links to both Map Viewer and Genomic BLAST pages.
|Non Canonical Base Pair Database" info|
The database provides access to all RNA structures in which a particular rare base pair has been found.
|Neuronal Ceroid Lipofuscinoses Mutation Database|
The database contains published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.
|Nucleic Acid Database" info|
The NDB shows nucleic acid-containing structures in a X-ray atlas and in a NMR-atlas.
|Neisseria meningitidis / MLST|
Database about Neisseria meningitidis.
|Parasitic Nematode Sequencing Project" info|
Nematode.net is a resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis.
|Nematode Sequence and Functional Data Database" info|
NEMBASE is a database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project.
|NetAffx Analysis Center" info|
NetAffx details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix.
A taxonomy database, integrating taxonomy data compiled at NCBI and data specific to the Swiss-Prot database.
|NONCODE - The Database Of All Kinds Of Noncoding RNA|
NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs).
|Noncoding RNAs Database|
Database with informations about noncoding RNA.
|Nucleosome Positioning Region Database (NPRD)" info|
Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database.
|Obesity Gene Map Database" info|
Database about genes involved in obesity.
|Ovarian Kaleidoscope Database" info|
The Ovarian Kaleidoscope database (OKdb) is a collaborative online resource for scientists investigating the ovary. It provides information regarding the biological function, expression pattern, and regulation of genes expressed in the ovary, as well as for the phenotypes associated with their mutation.
|Online Mendelian Inheritance in Man" info|
Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily.
|OMIM Morbid Map|
The OMIM Morbid Map presents the cytogenetic map location of disease genes described in OMIM.
OMIMALLELE contains alleles (mutations and polymorphisms) reported in OMIM.
Collection of ORFs that are sold by Invitrogen
|Phenylalanine Hydroxylase Locus Knowledgebase" info|
PAHdb is an locus-specific database for mutations in the human phenylalanine hydroxylase gene (symbol PAH) and the associated phenotypes at the levels of protein, metabolites and organism.
|Protein and Associated Nucleotide Domains with Inferred Trees" info|
PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
|Protein ANalysis THrough Evolutionary Relationships" info|
The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions.
Parasite - Genome database, produced by the 9712 Medical Center Drive Rockville, MD 20850
|European Mutant Mouse Pathology Database" info|
Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are also available.
|Cell Signaling Pathways|
Cell signaling pathways can be conveniently explored using PathFinder, an interactive, online graphical representation of cell signaling pathways.
"Pathway", the list of pathway maps is a part of the KEGG system. KEGG (Kyoto Encyclopedia of Genes and Genomes) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by the genome sequencing projects. The KEGG project is being undertaken in the Institute for Chemical Research, Kyoto University as a part of the Japanese Human Genome Program.
|Pathway Interaction Database|
Biomolecular interactions and cellular processes assembled into authoritative human signaling pathways.
|Pig EST Data Explorer" info|
Database of full-length enriched cDNA libraries and ESTs in pigs.
PepHMM is a hidden Markov Model based scoring function for mass spectrometry database search.
|Public Expression Profiling Resource (pepr)" info|
Public expression profiling resource provides expression profiles in a variety of diseases and conditions.
|The Plasmodium falciparum Genome Database|
Database about the Genome of the Malaria causing Plasmodium falciparum.
|Human Prostate Gene DataBase" info|
PGDB is a database of human genes related to the prostate and prostatic diseases.
PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene in this database allows the user to compare phenotypes of a gene over many organisms simultaneously.
|PHEX Locus Database" info|
Database about nucleotide variation found in the PHEX gene, the majority of which are found in patients with X-linked hypophosphatemia.
|PEDE - Pig cSNP Database|
Informations about SNPs in cDNA of the pig.
|The Plasmodium Genome Resource" info|
PlasmoDB is the official database of the malaria parasite genome project. This resource provides access to finished sequence for Plasmodium falciparum (strain 3D7), generated by the Sanger Institute, TIGR/NMRC, and Stanford, in addition to a wide range of related genomic-scale datasets from other sources.
|Mammalian mRNA Polyadenylation Database" info|
PolyA_DB is a database which provides several types of information regarding polyadenylation in mammalian species:
PolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
A PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via Sequin, often as a sequence alignment.
Ribosomal RNA-(rRNA)-targeted oligonucleotide probes are widely used for culture-independent identification of microorganisms in environmental and clinical samples. ProbeBase is a comprehensive database containing more than 700 published rRNA-targeted oligonucleotide probe sequences.
|PROkaryotIC Database Of Gene Regulation And Regulatory NETworks|
The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks.
|PROkaryotIC Database Of Gene Regulation And Regulatory NETworks" info|
The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks.
|Database of E. coli mRNA Promoters" info|
PromEC is a database of E. coli mRNA promoters with experimentally identified transcriptional start sites.
|PTCH1 Mutation Database|
Database about mutations and polymorphisms in the PTCH1 gene.
|Quantitative PCR Primer Database (QPPD)|
The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays. All data has been gathered from published articles, cited in PubMed. This resource is a collaborative effort of the NCI-Frederick Gene Expression Laboratory and the CGAP Genome Annotation Initiative.
|Rat Genome Database" info|
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
|Ribosomal Database Project|
The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
|Reactome - A Knowledgebase of Biological Processes|
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a resource of core pathways and reactions in human biology.
|The Restriction Enzyme Database" info|
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. REBASE was made by
Nobel laureate Dr. Richard J. Roberts and Dana Macelis.
|Database of the Translational Recoding Events (recode)" info|
The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information.
|Recurrent Chromosome Aberrations in Cancer|
The recurrent aberrations were derived from the Mitelman Database of Chromosome Aberrations in Cancer (2003) and include all cytogenetic changes present in at least two cases of the same morphologic entity, and, whenever applicable for solid tumors, within the same site. The complete karyotypes, patient characteristics, and references are found in the Mitelman Database of Chromosome Aberrations in Cancer.
|REFerence database for Gene EXpression Analysis" info|
Database for gene expression analysis.
|Reference Sequence (RefSeq)|
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
Repbase Update is a database of repetitive elements from diverse eukaryotic organisms.
|RNA Families Database of Alignments and CMs|
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
|Ribosomal RNA Database|
This database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.
|Ribosomal RNA BLAST|
Database about ribosomal RNA.
|Ribosomal Differentiation of Medical Microorganisms" info|
Database about the ribosomal differentiation of medical relevant microorganisms.
|RNA Databases / Israel Science and Technology Directory|
Compilation of RNA databases by the Israel Science and Technology Directory.
|RNA Modification Database|
The RNA Modification Database is a comprehensive list of post-transcriptionally modified nucleosides from RNA.
|Reactive Oxygen Species and Cell Signaling Pathway|
ROSPath is a database for proteins involved in ROS-mediated signaling pathways.
|Ribosomal Protein Gene Database" info|
RPG is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli.
|Real Time PCR Primer and Probe Database|
Database for real-time PCR primer and probe sequences.
|Science of Aging Database" info|
This database includes genes and interventions that have been studied with respect to their effects on life-span or age-related neurological diseases.
|Database for Repeat Prioritization" info|
Satellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia.
The database includes an initial set of eukaryotic genomic annotations, with special emphasis on the human selenoproteome, for immediate inspection by selenium researchers or incorporation into more general databases.
|Structure-Function Linkage Database" info|
|Stress-Induced DNA Duplex Destabilization (SIDD) - Database" info|
SIDDBASE is a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes.
|Comprehensive ribosomal RNA databases" info|
Ribosomal RNA database.
Database about Short interfering RNAs.
siRNA Database made by the Center for Genomics and Bioinformatics / Karolinska Institute.
|Stanford Microarray Database" info|
SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
|The SNP Consortium Database" info|
The SNP Consortium Ltd. is a non-profit foundation organized for the purpose of providing public genomic data. Its mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make the information related to these SNPs available to the public without intellectual property restrictions.
|SNP500 Cancer Database|
The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.
|Single Nucleotide Polymorphisms Database (SNPper)|
SNPper (pronounced 'snipper') is a web-based application to look for known Single Nucleotide Polymorphisms (SNPs) in public databases.
SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
|Signaling Pathway Integrated Knowledge Engine|
The rapid accumulation of knowledge on biological signaling pathways and their regulatory mechanisms has highlighted the need for specific repositories that can store, organize and allow retrieval of pathway information in a way that will be useful for the research community. SPIKE is a database for achieving this goal, containing highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction.
|Canonical and Non-Canonical Splice Site Sequences in Mammalian Genes" info|
SpliceDB is a database of known mammalian splice site sequences.
SpliceNest is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences from GeneNest to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA.
More then 300 molecular biology databases
|Signal Transductions Classification Database" info|
The Signal Transduction Classification Database (STCDB) is a database about to the classification of signal transduction.
|Short Tandem Repeat DNA|
While the use of STRs for genetic mapping and identity testing has become widespread among DNA typing laboratories, there is no single place where information may be found regarding STR systems. This web site is an attempt to bring together the abundant literature on the subject in a cohesive fashion to make future work in this field easier. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included in this database. Addresses for scientists and organizations working in this area have also been included as well as a comprehensive reference listing of material on STRs used for DNA typing purposes.
|Search Tool for the Retrieval of Interacting Genes / Proteins (STRING)|
STRING is a database of known and predicted protein-protein interactions.
|Subviral RNA Database" info|
SubViral RNA: a database of the smallest known auto-replicable RNA species.
TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA (ref. 1). As an option, nonconserved sites are also predicted.
|NCBI Taxonomy Database|
The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
|Human TBX5 Gene Mutation Database" info|
Germline mutations of the TBX5 gene were identified as the primary cause in up to 70% of patients with Holt-Oram syndrome (HOS), an autosomal dominant disorder characterized by malformations of the upper limbs and cardiac defects. The database informs about the genetic variations within the TBX5 gene. The databank is maintained by the Institute of Human Genetics, University of Leipzig, Germany.
|The Cancer Genome Atlas|
The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health, U.S. Department of Health and Human Services.
|Transcription Element Search System" info|
TESS is a web tool for predicting transcription factor binding sites in DNA sequences.
TFExplorer is a database for predicted regulatory elements in human, mouse, and rat. It shows predicted binding sites of transcription factors in the promoter regions, along with their phylogenetic footprinting information. In addition, TFExplorer can search for genes that have a given sequence pattern in their promoter regions using the motif-searching method.
|Third Party Annotation Sequence Database|
A TPA sequence is derived or assembled from primary sequence data currently found in the DDBJ/EMBL/GenBank International Nucleotide Sequence Collaboration Databases. It can be genomic or mRNA sequence, and can be assembled or derived from primary genomic and/or mRNA sequences.
|TIGR Gene Indices|
Organism-specific databases of EST and gene sequences.
|TIGR Comprehensive Microbial Resource" info|
The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals.
|TIGR Microbial Database|
The database contains lists of completed and ongoing genome projects with links to complete genome sequences.
The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called "10S RNA").
|Gene Expression in Tooth|
Database about the geneexpression in tooth.
|Topographic Database of Non-Synonymous SNPs" info|
This database allows visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations as described in Stitziel et. al. (JMB,327(5):1021-1030).
|TraitMap: Genetic-Map Database|
TraitMap contains curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana.
TRANSCompel is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signalling pathways.
|TRANSCompel® 6.0" info|
The TRANSCompel database emphasizes the key role of specific interactions between transcription factors binding to their target sites providing specific features of gene regulation in a particular cellular content.
|Transcription Factor Database|
TRANSFAC is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
|Genomic Comparisons of Membrane Transport Systems|
TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
|Database Of Tandem Repeats In The Human Genome" info|
The Database Of Tandem Repeats In The Human Genome is maintained by the Bioinformatics Centre, Washington Singer Laboratories, University of Exeter, UK.
|The Tandem Repeats Database|
Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats.
|Transcriptional Regulatory Element Database" info|
Transcriptional Regulatory Element Database (TRED) is a repository for both cis- and trans- regulatory elements in mammals.
|Tree of Life" info|
The Tree of Life is a collaborative web project, produced by biologists from around the world. On more than 2600 World Wide Web pages, the Tree of Life provides information about the diversity of organisms on Earth, their history, and characteristics.
|tRNA - Database|
Database about tRNA, hosted and maintained in a cooperation between the universities of Leipzig (Germany), Marburg (Germany) and Strasbourg (France).
|Transcription Regulatory Regions Database|
TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimental information is included into TRRD.
|Transcription Factor Database" info|
TrSDB-TranScout Database-(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation.
Database about the Genome of Mycobacterium tuberculosis.
|Turkish Human Mutation Database|
Database about human mutations of the turkish population.
UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
UniSTS is a NCBI resource that reports information about markers, or Sequence Tagged Sites (STS).
UniVec is a database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination). Screening using UniVec is efficient because a large number of redundant sub-sequences have been eliminated to create a database that contains only one copy of every unique sequence segment from a large number of vectors.
VBASE2 is a database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences.
|Viral Bioinformatics Resource Center & Viral Bioinformatics - Canada|
This resource provides access to viral genomes and a variety tools for comparative genomic analyses. At the heart of the system is VOCs (Virus Orthologous Clusters), a database with built-in tools that allows users to retrieve and analyze the genes, gene families, and genomes of 11 different virus families. The database is the source of information for other programs of the workbench for whole genome alignments, genome display, or gene/protein sequence analysis.
Characterization and classification of nucleic acid vectors.
|Comprehensive Viral Genome Resource" info|
Database for complete viral genome sequences.
|Virus-Specific Oligonucleotides Database" info|
VirOligo is a database of virus-specific oligonucleotides.
|Virtual Cell Animation Collection|
MOLECULAR AND CELLULAR BIOLOGY LEARNING CENTER
The lessons are produced in cooperation between the National Sience Foundation and the U.S. Department of Education.
|Visualizing Global DNA Sequence Alignments of Arbitrary Length" info|
VISTA is a program for visualizing global DNA sequence alignments of arbitrary length.
|WebQTL Project" info|
WebQTL stors data about gene expression, neuropharmacological,anatomical, and behavioral data for over 30 strains of mice.
WormBase is the central data repository for information about Caenorhabditis elegans and related nematodes.
WormBase is the central data repository for information about Caenorhabditis elegans and related nematodes.
|The Y-Chromosome Haplotype Reference Database" info|
The ability to identify male-specific DNA renders polymorphic Y-chromosomal sequences an invaluable addition to the standard panel of autosomal loci used in forensic genetics (Roewer 2009). Y-STR haplotyping is particularly important for sensitive typing of male DNA in mixed stains as well as for rapid assortment of biological crime scene evidence. Moreover, Y chromosomal profiling can trace back paternal lineages into the past and has thus been proven a useful tool in genealogical and kinship testing. The individuality of the male-specific part of the Y chromosome can be optimally explored by the Y-STR haplotype analysis using a set of highly variable short tandem repeat markers approved by the forensic and scientific community.