Biological databases are stores of biological information.

Primary sequence databases

The International Nucleotide Sequence Database

International Nucleotide Sequence Database Collaboration

The International Nucleotide Sequence Database Collaboration consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It involves the following computerized databases: DNA Data Bank of Japan , GenBank and the EMBL...

 (INSD) (http://www.insdc.org/) consists of the following databases.

1. DDBJ (DNA Data Bank of Japan)
2. EMBL Nucleotide Sequence DB (European Molecular Biology Laboratory
   European Molecular Biology Laboratory
   The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...
   
   )
3. GenBank
   GenBank
   The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
   
    http://www.ncbi.nlm.nih.gov/Genbank/index.html (National Center for Biotechnology Information
   National Center for Biotechnology Information
   The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
   
   )

The three databases, DDBJ (Japan), GenBank (USA) and EMBL Nucleotide Sequence Database (Europe), are repositories for nucleotide sequence

Primary structure

The primary structure of peptides and proteins refers to the linear sequence of its amino acid structural units. The term "primary structure" was first coined by Linderstrøm-Lang in 1951...

 data from all organism

Organism

In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

s. All three databases accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data.

Metadatabases

Strictly speaking a metadatabase

Metadatabase

Metadatabase is a database model for metadata management, global query of independent databases, and distributed data processing.This term is an addition to the dictionary. Originally, metadata is only a common term referring simply to "data about data", such as tags, keywords, and markup headers...

 can be considered a database of databases, rather than any one integration project or technology. They collect data from different sources and usually make them available in new and more convenient form, or with an emphasis on a particular disease or organism.

1. Entrez
   Entrez
   The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...
   
   http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi (National Center for Biotechnology Information
   National Center for Biotechnology Information
   The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
   
   )
2. euGenes (Indiana University
   Indiana University Bloomington
   Indiana University Bloomington is a public research university located in Bloomington, Indiana, in the United States. IU Bloomington is the flagship campus of the Indiana University system. Being the flagship campus, IU Bloomington is often referred to simply as IU or Indiana...
   
   )
3. GeneCards (Weizmann Inst.
   Weizmann Institute of Science
   The Weizmann Institute of Science , known as Machon Weizmann, is a university and research institute in Rehovot, Israel. It differs from other Israeli universities in that it offers only graduate and post-graduate studies in the sciences....
   
   )
4. SOURCE (Stanford University
   Stanford University
   The Leland Stanford Junior University, commonly referred to as Stanford University or Stanford, is a private research university on an campus located near Palo Alto, California. It is situated in the northwestern Santa Clara Valley on the San Francisco Peninsula, approximately northwest of San...
   
   )
5. mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
6. Bioinformatic Harvesterhttp://harvester.fzk.de (Karlsruhe Institute of Technology
   Karlsruhe Institute of Technology
   The Karlsruhe Institute of Technology is a German academic research and education institution with university status resulting from a merger of the university and the research center of the city of Karlsruhe. The university, also known as Fridericiana, was founded in 1825...
   
   ) - Integrating 26 major protein/gene resources.
7. MetaBase
   MetaBase
   MetaBase is a user-contributed database of biological databases, listing all the biological databases currently available on the internet. The initial release of MetaBase was derived entirely from the content of the Nucleic Acids Research 2007 Database Issue...
   
   http://BioDatabase.Org (KOBIC
   KOBIC
   KOBIC stands for the Korean Bioinformation Center. It is comparable to the US NCBI in America and EBI in Europe.The Korean Bioinformation Center was originally established as NGIC in 2001 in Korea...
   
   ) - A user contributed database of biological databases.
8. ConsensusPathDB
   ConsensusPathDB
   The ConsensusPathDB is a molecular functional interaction database, integrating information on protein interactions, signaling, metabolism and gene regulation in humans. ConsensusPathDB includes functional interactions from 12 databases...
   
    - A molecular functional interaction database, integrating information from 12 other databases.
9. PathogenPortal A repository linking to the Bioinformatics Resource Centers
   Bioinformatics Resource Centers
   The Bioinformatics Resource Centers are a group of five Internet-based research centers established in 2004 and funded by NIAID The BRCs were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in...
   
    (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID)
10. BioGraph (University of Antwerp
    University of Antwerp
    The University of Antwerp is one of the major Belgian universities located in the city of Antwerp. The name is sometimes abbreviated as UA.-History:...
    
    , Vlaams Instituut voor Biotechnologie) A knowledge discovery service based on the integration of over 20 heterogeneous biomedical knowledge bases

Genome databases

These databases collect organism genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 sequences, annotate and analyze them, and provide public access. Some add curation

Curation

Curation may refer to:*Digital curation, the preservation and maintenance of digital assets*Sheer curation, a minimalist form of digital curationCuration may also be:*The work performed by a curator*Archiving, historical record keeping...

 of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism

Model organism

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...

 genome.

1. Bioinformatic Harvester
2. SNPedia
   SNPedia
   SNPedia is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms . Each article on a SNP provides a short description, links to scientific articles and personal genomics web sites, as well as microarray information about that SNP...
   
   
3. CAMERA Resource for microbial genomics and metagenomics
4. Corn, the Maize Genetics and Genomics Database
5. EcoCyc a database that describes the genome and the biochemical machinery of the model organism
   Model organism
   A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
   
    E. coli K-12
6. Ensembl
   Ensembl
   Ensembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...
   
    provides automatic annotation databases for human, mouse, other vertebrate
   Vertebrate
   Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
   
    and eukaryote
   Eukaryote
   A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
   
    genomes.
7. PATRIC, the PathoSystems Resource Integration Center
8. Flybase
   FlyBase
   FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats...
   
   , genome of the model organism
   Model organism
   A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
   
    Drosophila melanogaster
   Drosophila melanogaster
   Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
   
   
9. MGI Mouse Genome (Jackson Lab.
   Jackson Laboratory
   The Jackson Laboratory was founded in Bar Harbor, Maine in 1929 by former University of Maine and University of Michigan president C. C. Little under the name Roscoe B...
   
   )
10. JGI Genomes of the DOE-Joint Genome Institute
    Joint Genome Institute
    The U.S. Department of Energy Joint Genome Institute was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory , Lawrence Livermore...
    
      provides databases of many eukaryote
    Eukaryote
    A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
    
     and microbial genomes.
11. National Microbial Pathogen Data Resource. A manually curated database of annotated genome data for the pathogens Campylobacter
    Campylobacter
    Campylobacter is a genus of bacteria that are Gram-negative, spiral, and microaerophilic. Motile, with either unipolar or bipolar flagella, the organisms have a characteristic spiral/corkscrew appearance and are oxidase-positive. Campylobacter jejuni is now recognized as one of the main causes...
    
    , Chlamydia
    Chlamydia (bacterium)
    Chlamydia is a genus of bacteria that are obligate intracellular parasites. Chlamydia infections are the most common bacterial sexually transmitted infections in humans and are the leading cause of infectious blindness worldwide....
    
    , Chlamydophila
    Chlamydophila
    Chlamydophila is a bacterial genus belonging to the family Chlamydiaceae, order Chlamydiales, class/phylum Chlamydiae.-Taxonomy:Chlamydophila was recognized in 1999, with six species in Chlamydophila and three in the original genus, Chlamydia...
    
    , Haemophilus
    Haemophilus
    Not to be confused with Haemophilia.Haemophilus is a genus of Gram-negative, pleomorphic, coccobacilli bacteria belonging to the Pasteurellaceae family. While Haemophilus bacteria are typically small coccobacilli, they are categorized as pleomorphic bacteria because of the wide range of shapes they...
    
    , Listeria, Mycoplasma
    Mycoplasma
    Mycoplasma refers to a genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many common antibiotics such as penicillin or other beta-lactam antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans,...
    
    , Neisseria
    Neisseria
    The Neisseria is a large genus of commensal bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens. N. meningitidis and N. gonorrhoeae often cause asymptomatic infections, a commensal-like behavior...
    
    , Staphylococcus
    Staphylococcus
    Staphylococcus is a genus of Gram-positive bacteria. Under the microscope they appear round , and form in grape-like clusters....
    
    , Streptococcus
    Streptococcus
    Streptococcus is a genus of spherical Gram-positive bacteria belonging to the phylum Firmicutes and the lactic acid bacteria group. Cellular division occurs along a single axis in these bacteria, and thus they grow in chains or pairs, hence the name — from Greek στρεπτος streptos, meaning...
    
    , Treponema
    Treponema
    Treponema is a bacterial genus. The major species is Treponema pallidum, whose subspecies are responsible for diseases such as syphilis and yaws.The species Treponema hyodysenteriae and Treponema innocens have been reclassified into Serpula....
    
    , Ureaplasma
    Ureaplasma
    Ureaplasma is a genus of bacteria belonging to the family Mycoplasmataceae. As the name imples, ureaplasma is urease positive.It includes the species:* Ureaplasma canigenitalium* Ureaplasma cati* Ureaplasma diversum...
    
    , and Vibrio
    Vibrio
    Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form...
    
    .
12. Saccharomyces Genome Database
    Saccharomyces Genome Database
    The Saccharomyces Genome Database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast....
    
    , genome of the yeast
    Yeast
    Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
    
     model organism.
13. Viral Bioinformatics Resource Center Curated database containing annotated genome data for eleven virus families.
14. The SEED platform for microbial genome analysis includes all complete microbial genomes, and most partial genomes. The platform is used to annotate microbial genomes using subsystems.
15. Xenbase
    Xenbase
    Xenbase is a model organism database, providing informatics resources, genomic and biological data on the frogs, Xenopus laevis and Xenopus tropicalis.-Xenopus as a model organism:...
    
    , genome of the model organism
    Model organism
    A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
    
     Xenopus tropicalis and Xenopus laevis
16. Wormbase
    WormBase
    WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes....
    
    , genome of the model organism
    Model organism
    A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
    
     Caenorhabditis elegans
    Caenorhabditis elegans
    Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
    
    
17. Zebrafish Information Network
    Zebrafish Information Network
    The Zebrafish Information Network is an online biological database of information about the zebrafish . The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data...
    
    , genome of this fish
    Fish
    Fish are a paraphyletic group of organisms that consist of all gill-bearing aquatic vertebrate animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish, as well as various extinct related groups...
    
     model organism.
18. TAIR, The Arabidopsis Information Resource.
19. UCSC Malaria Genome Browser
    UCSC Malaria Genome Browser
    UCSC Malaria Genome Browser is a bioinformatic research tool to study the malaria genome, developed by Hughes Undergraduate Research Laboratory together with the laboratory of Prof. Manuel Ares Jr. at the University of California, Santa Cruz....
    
    , genome of malaria causing species (Plasmodium falciparumata and others)
20. RGD Rat Genome Database
    Rat genome database
    The Rat Genome Database is a collection of genetic and genomic information on the rat. Development and maintenance of RGD began in 1995 and is funded by the United States National Institutes of Health and hosted at the Medical College of Wisconsin...
    
    : Genomic and phenotype data for Rattus norvegicus
21. http://integrall.bio.ua.pt INTEGRALL: Database dedicated to integrons, bacterial genetic elements involved in the antibiotic resistance
22. Fourmidable ant genome database provides ant genome blast search and sequence download.
23. VectorBase The NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
    VectorBase
    is one of the five Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health , which is an agency of the United States Department of Health and Human Services...
    
    

Protein sequence databases

1. UniProt
   UniProt
   UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
   
   http://www.uniprot.org Universal Protein
   Protein
   Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
   
    Resource (UniProt Consortium: EBI
   European Bioinformatics Institute
   The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
   
   , Expasy, PIR
   Protein Information Resource
   The Protein Information Resource , located at Georgetown University Medical Center , is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies-History:...
   
   )
2. PIR Protein Information Resource (Georgetown University
   Georgetown University
   Georgetown University is a private, Jesuit, research university whose main campus is in the Georgetown neighborhood of Washington, D.C. Founded in 1789, it is the oldest Catholic university in the United States...
   
    Medical Center (GUMC))
3. Swiss-Prothttp://www.expasy.org/sprot/ Protein Knowledgebase (Swiss Institute of Bioinformatics
   Swiss Institute of Bioinformatics
   The Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland...
   
   )
4. PEDANT Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit)
5. PROSITE Database of Protein Families
   Protein family
   A protein family is a group of evolutionarily-related proteins, and is often nearly synonymous with gene family. The term protein family should not be confused with family as it is used in taxonomy....
   
    and Domains
6. DIP Database of Interacting Proteins (Univ. of California
   University of California
   The University of California is a public university system in the U.S. state of California. Under the California Master Plan for Higher Education, the University of California is a part of the state's three-tier public higher education system, which also includes the California State University...
   
   )
7. Pfam Protein families database of alignments and HMMs (Sanger Institute
   Sanger Institute
   The Wellcome Trust Sanger Institute is a non-profit, British genomics and genetics research institute, primarily funded by the Wellcome Trust....
   
   )
8. PRINTS PRINTS is a compendium of protein fingerprints (Manchester University)
9. ProDom Comprehensive set of Protein Domain Families (INRA
   Institut National de la Recherche Agronomique
   The Institut National de la Recherche Agronomique is a French public research institute dedicated to scientific studies surrounding the problems of agriculture...
   
   /CNRS
   Centre national de la recherche scientifique
   The National Center of Scientific Research is the largest governmental research organization in France and the largest fundamental science agency in Europe....
   
   )
10. SignalP 3.0 Server for signal peptide
    Signal peptide
    A signal peptide is a short peptide chain that directs the transport of a protein.Signal peptides may also be called targeting signals, signal sequences, transit peptides, or localization signals....
    
     prediction (including cleavage site prediction), based on artificial neural network
    Artificial neural network
    An artificial neural network , usually called neural network , is a mathematical model or computational model that is inspired by the structure and/or functional aspects of biological neural networks. A neural network consists of an interconnected group of artificial neurons, and it processes...
    
    s and HMMs
11. SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms
12. Annotation Clearing House a project from the National Microbial Pathogen Data Resource
    National Microbial Pathogen Data Resource
    The was one of the eight Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health , which is an agency of the United States Department of Health and Human Services.The NMPDR was funded for five...
    
    

Protein structure

Protein structure

Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...

 databases

1. Protein Data Bank
   Protein Data Bank
   The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
   
   http://www.rcsb.org/pdb/ (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB))
2. SCOP Structural Classification of Proteins
   Structural Classification of Proteins
   The Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
   
   
3. CATH Protein Structure Classification

Protein model

Protein structure prediction

Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...

 databases

1. SWISS-MODEL Server and Repository for Protein Structure Models
2. ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF
   University of California, San Francisco
   The University of California, San Francisco is one of the world's leading centers of health sciences research, patient care, and education. UCSF's medical, pharmacy, dentistry, nursing, and graduate schools are among the top health science professional schools in the world...
   
   )
3. Protein Model Portalhttp://proteinmodelportal.org (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland)

Carbohydrate

Carbohydrate

A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...

 structure databases

1. EuroCarbDB
   Eurocarbdb
   EuroCarbDB is an EU-funded initiative for the creation of software and standards for the systematic collection of carbohydrate structures and their experimental data...
   
   http://www.ebi.ac.uk/eurocarb, A repository for both carbohydrate sequences/structures and experimental data.

Protein-protein interaction

Protein-protein interaction

Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...

s

1. BioGRID
   BioGRID
   The Biological General Repository for Interaction Datasets is a curated biological database of protein-protein and genetic interactions created in 2003 The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions...
   
    http://www.thebiogrid.org A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute
   Samuel Lunenfeld Research Institute
   The Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada was established in 1985 by an endowment from the Lunenfeld and Kunin families. It comprises 36 principal investigators, has a budget of C$90 million , has over 200 trainees and approximately 600 staff...
   
   )
2. STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL
   European Molecular Biology Laboratory
   The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...
   
   )
3. DIP Database of Interacting Proteins
4. BIND Biomolecular Interaction Network Database
5. NetPro
6. CCSB Interactome

Signal transduction pathway databases

• Cancer Cell Map
• Netpath
  Netpath
  NetPath is a manually curated resource of human signal transduction pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University and the Institute of Bioinformatics , Bangalore, India, and is also worked on by other parties....
  
   - A curated resource of signal transduction pathways in humans
• Reactome
  Reactome
  Reactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
  
  
• NCI-Nature Pathway Interaction Database
  NCI-Nature Pathway Interaction Database
  The is a free biomedical database of human cellular signaling pathways. The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment. The database was...
  
  
• SignaLink Database
• WikiPathways
  WikiPathways
  WikiPathways is a community resource for biological pathways.-What is WikiPathways:WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways represents a new model for pathway databases that enhances complementary...
  
  

Metabolic pathway

Metabolic pathway

In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...

 databases

1. BioCyc Database Collection
   BioCyc Database Collection
   The BioCyc database collection is a set of biological databases. Databases within BioCyc describe genome and pathway information for individual organisms. BioCyc is maintained by SRI International, in Menlo Park, California....
   
    including EcoCyc
   EcoCyc
   EcoCyc is a bioinformatics database for the bacterium Escherichia coli K-12. The EcoCyc project performs literature-based curation of the E. coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways....
   
    and MetaCyc
   MetaCyc
   The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc stores experimentally determined metabolic pathways....
   
   
2. KEGG PATHWAY Database
   KEGG PATHWAY Database
   KEGG is a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The PATHWAY database records networks of molecular interactions in the cells, and variants of them specific to particular organisms...
   
   http://www.genome.ad.jp/kegg/pathway.html (Univ. of Kyoto
   Kyoto University
   , or is a national university located in Kyoto, Japan. It is the second oldest Japanese university, and formerly one of Japan's Imperial Universities.- History :...
   
   )
3. MANET database
   MANET database
   The Molecular Ancestry Network database is a bioinformatics database that maps evolutionary relationships of protein architectures directly onto biological networks. It was originally developed by Hee Shin Kim, Jay E...
   
    http://www.manet.uiuc.edu/ (University of Illinois)
4. Reactome
   Reactome
   Reactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
   
   http://www.reactome.org (Cold Spring Harbor Laboratory
   Cold Spring Harbor Laboratory
   The Cold Spring Harbor Laboratory is a private, non-profit institution with research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics. The Laboratory has a broad educational mission, including the recently established Watson School of Biological Sciences. It...
   
   , EBI
   European Bioinformatics Institute
   The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
   
   , Gene Ontology Consortium)

Microarray databases

1. ArrayExpress (European Bioinformatics Institute
   European Bioinformatics Institute
   The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
   
   )
2. Gene Expression Omnibus (National Center for Biotechnology Information
   National Center for Biotechnology Information
   The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
   
   )
3. GPX(Scottish Centre for Genomic Technology and Informatics)
4. maxd (Univ. of Manchester
   University of Manchester
   The University of Manchester is a public research university located in Manchester, United Kingdom. It is a "red brick" university and a member of the Russell Group of research-intensive British universities and the N8 Group...
   
   )
5. Stanford Microarray Database (SMD) (Stanford University
   Stanford University
   The Leland Stanford Junior University, commonly referred to as Stanford University or Stanford, is a private research university on an campus located near Palo Alto, California. It is situated in the northwestern Santa Clara Valley on the San Francisco Peninsula, approximately northwest of San...
   
   )

Mathematical model databases

1. Biomodels Database
   BioModels Database
   BioModels Database is a free and open-source database for storing, exchanging and retrieving published quantitative models of biological interest...
   
   
2. CellML

PCR / real time PCR primer

Primer (molecular biology)

A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...

 databases

1. PathoOligoDB: A free QPCR oligo database for pathogens

Specialized databases

• Antibody Central Antibody information database and search resource.
• BIOMOVIE (ETH Zurich
  ETH Zurich
  The Swiss Federal Institute of Technology Zurich or ETH Zürich is an engineering, science, technology, mathematics and management university in the City of Zurich, Switzerland....
  
  ) movies related to biology and biotechnology
• CGAP Cancer Genes (National Cancer Institute
  National Cancer Institute
  The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...
  
  )
• Clone Registry Clone Collections (National Center for Biotechnology Information
  National Center for Biotechnology Information
  The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
  
  )
• Connectivity map Transcriptional expression data and correlation tools for drugs
• CTD The Comparative Toxicogenomics Database
  Comparative Toxicogenomics Database
  The Comparative Toxicogenomics Database is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases....
  
   describes chemical-gene-disease interactions
• DBGET H.sapiens (Univ. of Kyoto
  Kyoto University
  , or is a national university located in Kyoto, Japan. It is the second oldest Japanese university, and formerly one of Japan's Imperial Universities.- History :...
  
  )
• DiProDB
  DiProDB
  DiProDB is a database designed to collect and analyse thermodynamic, structural and other dinucleotide properties....
  
   A database to collect and analyse thermodynamic, structural and other dinucleotide properties.
• Drug2Gene Provides integrated information for identified and reported relations between genes/proteins and drugs/compounds
• Dryad a repository of data underlying scientific publications in the basic and applied biosciences.
• Edinburgh Mouse Atlas
• GreenPhylDB (A phylogenomic database for plant comparative genomics)
• GDB Hum. Genome Db (Human Genome Organisation
  Human Genome Organisation
  The Human Genome Organisation is an organization involved in the Human Genome Project, a project about mapping the human genome. HUGO was established in 1989 as an international organization, primarily to foster collaboration between genome scientists around the world...
  
  )
• HGMD disease-causing mutations (HGMD Human Gene Mutation Database)
• HUGO (Official Human Genome Database: HUGO Gene Nomenclature Committee)
• HvrBase++ Human and primate mitochondrial DNA
• INTERFEROME The Database of Interferon Regulated Genes
• List with SNP-Databases
• Minimotif Miner
  Minimotif Miner
  Minimotif Miner is a program and database designed to identify minimotifs in any protein. Minimotifs are short contiguous peptide sequences that are known to have a function in at least one protein. Minimotifs are also called sequence motifs or short linear motifs or SLiMs. These are generally...
  
   -Database of short contiguous functional peptide motifs
• NCBI-UniGene (National Center for Biotechnology Information)
• Oncogenomic databases
  Databases for oncogenomic research
  Databases for oncogenomic research are biological databases dedicated to cancer data and oncogenomic research. They can be a primary source of cancer data, offer a certain level of analysis or even offer online data mining....
  
   A compilation of databases that serve for cancer research.
• OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
• OrthoMaM (A database of Orthologous Mammalian Markers)
• p53 The p53 Knowledgebase
• PhenCode linking human mutations with phenotype
• PhenomicDB multi-organism database linking genotype to phenotype
• Plasma Proteome Database Human plasma proteins along with their isoforms
• PolygenicPathways Genes and risk factors implicated in Alzheimer's disease, Bipolar disorder, Autism or Schizophrenia, multiple sclerosis and Parkinson's disease
• SHMPD The Singapore Human Mutation and Polymorphism Database
• SciClyc An Open-access database to shared antibodies, cell cultures, and documents for biomedical research.
• SNPSTR database A database of SNPSTRs - compound genetic markers consisting of a microsatellite (STR) and one tightly linked SNP - in human, mouse, rat, dog and chicken.
• TDR Targets
  TDR Targets
  The TDR Targets database is a bioinformatics project that seeks to exploit the availability of diverse genomic and chemical datasets to facilitate the identification and prioritization of drugs and drug targets in neglected disease pathogens...
  
   A chemogenomics database focused on drug discovery in tropical diseases.
• TRANSFAC
  TRANSFAC
  TRANSFAC is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites....
  
   A database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
• TreeBASE An open-access database of phylogenetic trees and the data behind them
• XTractor Discovering Newer Scientific Relations Across PubMed Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in PubMed.

Wiki-style databases

1. CHDwiki
2. EcoliWiki
3. Gene Wiki
   Gene Wiki
   The Gene Wiki is a project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles.-Number of gene articles:...
   
   
4. GyDB
5. OpenWetWare
6. PDBWiki
7. Proteopedia
8. Topsan
9. WikiGenes
10. WikiPathways
11. WikiProfessional
    WikiProfessional
    WikiProfessional is a web-based research environment for semantic searching, providing an intuitive tool for analyzing and relating concepts....
    
    
12. YTPdb