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ENSEMBL GENOME DATABASE PROJECT is a joint scientific project between the European Bioinformatics Institute
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 . After 10 years in existence, Ensembl's aim remains to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms . Ensembl
Ensembl
is one of several well known genome browsers for the retrieval of genomic information.

Similar databases and browsers are found at NCBI and the University of California, Santa Cruz (UCSC) .

CONTENTS

* 1 Background * 2 Displaying genomic data * 3 Alternative access methods * 4 Current species * 5 See also * 6 References * 7 External links

BACKGROUND

The human genome consists of three billion base pairs , which code for approximately 20,000–25,000 genes . However the genome alone is of little use, unless the locations and relationships of individual genes can be identified. One option is manual annotation , 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 of protein to DNA
DNA
.

In the Ensembl
Ensembl
project, sequence data are fed into the gene annotation system (a collection of software "pipelines" written in Perl ) which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis and display. Ensembl
Ensembl
makes these data freely accessible to the world research community. All the data and code produced by the Ensembl
Ensembl
project is available to download, and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl
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 such as mouse , fruitfly and zebrafish ) as well as a wider range of genomic data, including genetic variations and regulatory features. Since April 2009, a sister project, Ensembl Genomes , has extended the scope of Ensembl
Ensembl
into invertebrate metazoa , plants , fungi , bacteria , and protists , whilst the original project continues to focus on vertebrates.

DISPLAYING GENOMIC DATA

Gene
Gene
SGCB aligned to the human genome

Central to the Ensembl
Ensembl
concept is the ability to automatically generate graphical views of the alignment of genes and other genomic data against a reference genome . 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 karyotypes down to text-based representations of DNA
DNA
and amino acid sequences, or present other types of display such as trees 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, either via a DAS (Distributed Annotation
Annotation
System ) server on the internet, or by uploading a suitable file in one of the supported formats, such as BAM , BED , or PSL .

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
Ensembl
provides a Perl API
API
(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
API
is used internally by the web interface to display the data. It is divided in sections like the core API, the compara API
API
(for comparative genomics data), the variation API
API
(for accessing SNPs, SNVs, CNVs..), and the functional genomics API
API
(to access regulatory data). The Ensembl
Ensembl
website provides extensive information on how to install and use the API.

This software can be used to access the public MySQL 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 an 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 most fully sequenced vertebrates and selected model organisms. All of them are eukaryotes, there are no prokaryotes. As of 2008 , this includes:

* Chordata
Chordata

* Mammalia
Mammalia

* Euarchontoglires

* Primates
Primates
: bushbaby , chimp , human, macaque , mouse lemur , orangutan , tarsier ; * Scandentia
Scandentia
: tree shrew ; * Glires (= Rodents + Lagomorphs): guineapig , kangaroo rat , mouse , rat , ground squirrel , pika , rabbit ;

* Laurasiatheria : cow , dolphin , alpaca , pig , cat , dog , horse , megabat , microbat , hedgehog , shrew ; * Afrotheria: elephant , hyrax , tenrec * Xenarthra
Xenarthra
: armadillo , sloth ; * Marsupialia : opossum , wallaby ; * Monotremes
Monotremes
: platypus ;

* Birds
Birds
: chicken , zebra finch ; * Lepidosauria : anole lizard (pre); * Lissamphibia : _Xenopus tropicalis_; * Teleost fishes: _Takifugu rubripes_ (fugu ), _Tetraodon nigroviridis _ (green spotted pufferfish), _Danio rerio_ (zebrafish ), _Oryzias latipes_ (medaka ), _Gasterosteus aculeatus_ (stickleback ); * Cyclostomata
Cyclostomata
: _Petromyzon marinus_ (sea lamprey ) (pre); * Tunicates
Tunicates
: _Ciona intestinalis_, _Ciona savignyi_;

* Non-vertebrates

* Insects
Insects
: _ Drosophila melanogaster
Drosophila melanogaster
_ (fruitfly), _Anopheles gambiae_ (mosquito), _Aedes aegypti_ (mosquito) * Worm
Worm
: _ Caenorhabditis elegans _

* Yeast
Yeast
: _ Saccharomyces cerevisiae
Saccharomyces cerevisiae
_ (baker's yeast)

SEE ALSO

* List of sequenced eukaryotic genomes * Sequence analysis * Sequence profiling tool * Sequence motif * UCSC Genome
Genome
Browser

REFERENCES

* ^ Hubbard T.; et al. (January 2002). "The Ensembl
Ensembl
genome database project". _Nucleic Acid Res_. 30 (1): 38–41. PMC 99161  _. PMID 11752248 . doi :10.1093/nar/30.1.38 . Retrieved 11 November 2014. * ^ Flicek P, Amode MR, Barrell D, et al. (November 2010). "Ensembl 2011" . Nucleic Acids Res_. 39 ( Database
Database
issue): D800–D806. PMC 3013672  _. PMID 21045057 . doi :10.1093/nar/gkq1064 . * ^ Flicek P, Aken BL, Ballester B, et al. (January 2010). "Ensembl\'s 10th year" . Nucleic Acids Res_. 38 ( Database
Database
issue): D557–62. PMC 2808936  _. PMID 19906699 . doi :10.1093/nar/gkp972 .

* ^ Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul (January 2017). " Ensembl
Ensembl
core software resources: storage and programmatic access for DNA
DNA
sequence and genome annotation". Database_. 2017 (1). doi :10.1093/database/bax020 . * ^ Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E (February 2004). "The Ensembl
Ensembl
Core Software Libraries". _Genome Research_. 14 (5): 929–933. PMC 479122  . PMID 15123588 . doi :10.1101/gr.1857204 .

EXTERNAL LINKS

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