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Ensembl genome database project is a scientific project at the
European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...
, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
s of our own species and other
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
s and
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 model organism will provide insight into the workings of other organisms. Mo ...
s. Ensembl is one of several well known genome browsers for the retrieval of
genomic Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...
information. Similar
database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
s and browsers are found at
NCBI The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is loca ...
and the University of California, Santa Cruz (UCSC).


History

The human genome consists of three billion
base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
s, which code for approximately 20,000–25,000
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s. However the genome alone is of little use, unless the locations and relationships of individual genes can be identified. One option is manual
annotation An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented Marginalia, in the margin of book page ...
, whereby a team of scientists tries to locate genes using experimental data from scientific journals and public databases. However this is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers to do the complex
pattern-matching In computer science, pattern matching is the act of checking a given sequence of tokens for the presence of the constituents of some pattern. In contrast to pattern recognition, the match usually must be exact: "either it will or will not be a ...
of
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
to
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. The Ensembl project was launched in 1999 in response to the imminent completion of the
Human Genome Project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...
, with the initial goals of automatically annotate the human genome, integrate this annotation with available biological data and make all this knowledge publicly available. In the Ensembl project, sequence data are fed into the gene annotation system (a collection of software "pipelines" written in
Perl Perl is a high-level, general-purpose, interpreted, dynamic programming language. Though Perl is not officially an acronym, there are various backronyms in use, including "Practical Extraction and Reporting Language". Perl was developed ...
) which creates a set of predicted gene locations and saves them in a
MySQL MySQL () is an Open-source software, open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A rel ...
database for subsequent analysis and display. Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data. Over time the project has expanded to include additional species (including key
model organisms 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 model organism will provide insight into the workings of other organisms. Mo ...
such as
mouse A mouse (: mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus'' ...
, fruitfly and
zebrafish The zebrafish (''Danio rerio'') is a species of freshwater ray-finned fish belonging to the family Danionidae of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (an ...
) as well as a wider range of genomic data, including
genetic variation Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources ...
s and regulatory features. Since April 2009, a sister project, Ensembl Genomes, has extended the scope of Ensembl into invertebrate
metazoa Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia (). With few exceptions, animals consume organic material, breathe oxygen, have myocytes and are able to move, can reproduce sexually, and grow from a hol ...
,
plants Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars f ...
,
fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
,
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
, and
protists A protist ( ) or protoctist is any Eukaryote, eukaryotic organism that is not an animal, Embryophyte, land plant, or fungus. Protists do not form a Clade, natural group, or clade, but are a Paraphyly, paraphyletic grouping of all descendants o ...
, focusing on providing taxonomic and evolutionary context to genes, whilst the original project continues to focus on vertebrates. As of 2020, Ensembl supported over 50 000 genomes across both Ensembl and Ensembl Genomes databases, adding some new innovative features such a
Rapid Release
a new website designed to make genome annotation data available more quickly to users, an

a new website to access to
SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. The virus previously had the Novel coronavirus, provisional nam ...
reference genome.


Displaying genomic data

Central to the Ensembl concept is the ability to automatically generate graphical views of the alignment of genes and other genomic data against a
reference genome A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the genome, set of genes in one idealized individual organism of a species. As they are a ...
. These are shown as data tracks, and individual tracks can be turned on and off, allowing the user to customise the display to suit their research interests. The interface also enables the user to zoom in to a region or move along the genome in either direction. Other displays show data at varying levels of resolution, from whole
karyotype A karyotype is the general appearance of the complete set of chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is discerned by de ...
s down to text-based representations of DNA and
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
sequences, or present other types of display such as
trees In botany, a tree is a perennial plant with an elongated stem, or trunk, usually supporting branches and leaves. In some usages, the definition of a tree may be narrower, e.g., including only woody plants with secondary growth, only p ...
of similar genes ( homologues) across a range of species. The graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA. Externally produced data can also be added to the display by uploading a suitable file in one of the supported formats, such as BAM, BED, or
PSL PSL may refer to: Sport *Pakistan Super League, a Twenty20 cricket league *Palau Soccer League, top division association football league in Palau *Pilipinas Super League, a professional basketball league *Philippine Super Liga, a defunct profes ...
. Graphics are generated using a suite of custom Perl modules based on GD, the standard Perl graphics display library.


Alternative access methods

In addition to its website, Ensembl provides a REST
API An application programming interface (API) is a connection between computers or between computer programs. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build ...
and a Perl
API An application programming interface (API) is a connection between computers or between computer programs. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build ...
(Application Programming Interface) that models biological objects such as genes and proteins, allowing simple scripts to be written to retrieve data of interest. The same API is used internally by the web interface to display the data. It is divided into sections like the core API, the compara API (for
comparative genomics Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach c ...
data), the variation API (for accessing SNPs, SNVs, CNVs..), and the functional genomics API (to access regulatory data). The Ensembl website provides extensive information o
how to install and use the API
This software can be used to access the public
MySQL MySQL () is an Open-source software, open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A rel ...
database, avoiding the need to download enormous datasets. The users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema. Large datasets can be retrieved using the BioMart data-mining tool. It provides a web interface for downloading datasets using complex queries. Last, there is a
FTP
server which can be used to download entire MySQL databases as well some selected data sets in other formats.


Current species

The annotated genomes include the most fully sequenced vertebrates and selected model organisms. All of them are eukaryotes, there are no prokaryotes. As of 2022, there are 271 species registered, this includes:


Open source/mirrors

All data part of the Ensembl project is open access and all software is open source, being freely available to the scientific community, under a CC BY 4.0 license. Currently, Ensembl database website is mirrored at three different locations worldwide to improve the service.


See also

* List of sequenced eukaryotic genomes * List of biological databases *
Sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome ...
*
Sequence profiling tool A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and ...
*
Sequence motif In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''A ...
* UCSC Genome Browser *
ENCODE The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims "to build a comprehensive parts list of functional elements in the human genome." ENCODE also supports further biomedical research by "generating community resourc ...


References


External links

*
VegaPre-EnsemblEnsembl genomesUCSC Genome BrowserNCBIEnsembl: Browsing chordate genomes on EBI Train OnLine
{{Authority control Genetic engineering in the United Kingdom Genome databases Medical databases in the United Kingdom Medical genetics Science and technology in Cambridgeshire South Cambridgeshire District Wellcome Trust Biological databases Bioinformatics Computational biology