Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species. The project is run by 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 ...

, and was launched in 2009 using the

Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

technology. The main objective of the Ensembl Genomes database is to complement the main Ensembl database by introducing five additional web pages to include genome data for

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 ...

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 ...

, 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 ...

plant Plants are the eukaryotes that form the Kingdom (biology), kingdom Plantae; they are predominantly Photosynthesis, photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with c ...

s, and

protist A protist ( ) or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a paraphyletic grouping of all descendants of the last eukaryotic common ancest ...

s. For each of the domains, the

tools are available for manipulation, analysis and visualization of genome data. Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online. Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. Ensembl and Ensembl Genomes software uses an Apache 2.0 license license.

Displaying genomic data

The key feature of Ensembl Genomes is its graphical interface, which allows users to scroll through a

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 ...

and observe the relative location of features such as conceptual

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 ...

(e.g.

genes 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 ...

, SNP loci), sequence patterns (e.g. repeats) and experimental data (e.g. sequences and external sequence features mapped onto the

). Graphical views are available for varying levels of resolution from an entire

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 ...

, down to the sequence of a single

exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence ...

. Information for a

is spread over four tabs, a species page, a ‘Location’ tab, a ‘

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 ...

’ tab and a ‘ Transcript’ tab, each providing information at a higher resolution. Searching for a particular species using Ensembl Genomes redirects to the species page. Often, a brief description of the species is provided, as well as links to further information and statistics about the

, the graphical interface and some of the tools available. A

is available for some species in Ensembl Genomes. If the karyotype is available there will be a link to it in the Gene Assembly section of the species page. Alternatively if users are in the ‘Location’ tab they can also view the karyotype by selecting ‘Whole genome’ in the left-hand menu. Users can click on a location within the karyotype to zoom in to one specific chromosome or a genomic region. This will open the ‘Location’ Tab. In the 'Location' tab, users can browse

, variations,

sequence conservation In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ( ...

, and other types of

along the

. The 'Region in detail' is highly configurable and scalable, and users can choose what they want to see by clicking on the 'Configure this page' button at the bottom of the left-hand menu. By adding and removing tracks users will be able to select the type of data they want to have included in the displays. Data from the following categories can be easily added or removed from this 'Location' tab view: '

Sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is cal ...

and assembly', '

Genes 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 ...

and transcripts', '

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

and

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 ...

alignments', 'Other

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 ...

alignments', '

Germline In biology and genetics, the germline is the population of a multicellular organism's cells that develop into germ cells. In other words, they are the cells that form gametes ( eggs and sperm), which can come together to form a zygote. They dif ...

variation', '

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 ...

', among others. Users can also change the display options such as the width. A further option allows users to reset the configuration back to the default settings. More specific information about a select

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 ...

can be found in the ‘Gene’ tab. Users can get to this page by searching for desired gene in the search bar and clicking on the gene ID or by clicking on one of the genes shown in the ‘Location’ tab view. The ‘Gene’ tab contains gene-specific information such as gene structure, number of transcripts, position on the

chromosome A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most import ...

and homology information in the form of gene trees. This information can be accessed via the menu on the left-hand side. A 'Transcript' tab will also appear when a user chooses to view a gene. The 'Transcript' tab contains much of the same information as the 'Gene' tab, however it is focused on only one transcript.

Tools

Adding Custom tracks to Ensembl Genomes

Ensembl Genomes allows comparing and visualising user data while browsing karyotypes and genes. Most Ensembl Genomes views include an ‘Add your data’ or ‘Manage your data’ button that will allow the user to upload new tracks containing reads or sequences to Ensembl Genomes or to modify data that has been previously uploaded. The uploaded data can be visualised in region views or over the whole karyotype. The uploaded data can be localised using Chromosome Coordinates or BAC Clone Coordinates. The following methods can be used to upload a data file to any Ensembl Genomes page: # Files smaller than 5 MB can be either uploaded directly from any computer or from a web location (URL) to the Ensembl servers. # Larger files can only be uploaded from web locations (URL). # BAM files can only be uploaded using the URL-based approach. The index file (.bam.bai) should be located in the same webserver. # A Distributed Annotation System source can be attached from web locations. The following file types are supported by Ensembl Genomes: * BED * BedGraph * Generic * GFF/GTF * PSL * WIG * BAM * BigBed * BigWig * VCF The data is uploaded temporarily into the servers. Registered users can log in and save their data for future reference. It is possible to share and access the uploaded data using and an assigned URL. Users are also allowed to delete their custom tracks from Ensembl Genomes.

BioMart

BioMart is a programming free search engine incorporated in Ensembl and Ensembl Genomes (except for Ensembl Bacteria) for the purpose of mining and extracting genomic data from the Ensembl databases in table formats like HTML, TSV, CSV or XLS. Release 45 (2019) of Ensembl Genomes has the following data available at the BioMarts: * Ensembl Protists BioMart: includes 33 species and variations for ''

Phytophthora infestans ''Phytophthora infestans'' is an oomycete or Oomycete, water mold, a fungus-like microorganism that causes the serious potato and tomato disease known as late blight or potato blight. Early blight, caused by ''Alternaria solani'', is also often c ...

'' and '' Phaeodactylum tricornutum'' * Ensembl Fungi BioMart: includes 56 species and variations for ''

Fusarium graminearum ''Gibberella zeae'', also known by the name of its anamorph ''Fusarium graminearum'', is a fungal plant pathogen which causes fusarium head blight (FHB), a devastating disease on wheat and barley. The pathogen is responsible for billions of doll ...

'', ''

Fusarium oxysporum ''Fusarium oxysporum'' (Schlecht as emended by Snyder and Hansen), an ascomycete fungus, comprises all the species, varieties and forms recognized by Wollenweber and Reinking within an infrageneric grouping called section Elegans. It is part of ...

'', ''

Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically meas ...

'', '' Puccinia graminis'', '' Verticillium dahliae'', ''

Zymoseptoria tritici ''Zymoseptoria tritici'', synonyms ''Septoria tritici'', ''Mycosphaerella graminicola'', is a species of filamentous fungus, an ascomycete in the family ''Mycosphaerellaceae''. It is a wheat plant pathogen causing septoria leaf blotch that is di ...

'', and ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungal microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have be ...

'' * Ensembl Metazoa BioMart: includes 78 species and variations for ''

Aedes aegypti ''Aedes aegypti'' ( or from Greek 'hateful' and from Latin, meaning 'of Egypt'), sometimes called the Egyptian mosquito, dengue mosquito or yellow fever mosquito, is a mosquito that spreads diseases like dengue fever, yellow fever, malar ...

'', ''

Anopheles gambiae The ''Anopheles gambiae'' complex consists of at least seven morphologically indistinguishable species of mosquitoes in the genus ''Anopheles''. The complex was recognised in the 1960s and includes the most important vectors of malaria in sub- ...

'' and ''

Ixodes scapularis ''Ixodes scapularis'' is a hard-bodied tick found in much of the eastern half of North America. It is commonly known as the deer tick, owing to its habit of parasitizing the white-tailed deer. It is also sometimes known as the black-legged tick ( ...

'' * Ensembl Plants: includes 67 species and variations for ''

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...

'', ''

Brachypodium distachyon ''Brachypodium distachyon'', commonly called purple false brome or stiff brome, is a grass species native to southern Europe, northern Africa and southwestern Asia east to India. It is related to the major cereal grain species wheat, barley, oats ...

'', '' Hordeum vulgare'', ''

Oryza glaberrima ''Oryza glaberrima'', commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown in West Africa around 3,000 years ago. In agriculture, it has largely been replaced by higher-yielding Asian ric ...

'', '' Oryza glumipatula'', ''Oryoza sativa indica'', ''Oryza sativa japonica'', '' Solanum lycopersicum'', ''

Sorghum bicolor ''Sorghum bicolor'', commonly called sorghum () and also known as great millet, broomcorn, guinea corn, durra, imphee, jowar, or milo, is a species in the grass genus ''Sorghum'' cultivated for its grain. The grain is used as food by humans, ...

'', '' Triticum aestivum'', ''

Vitis vinifera ''Vitis vinifera'', the common grape vine, is a species of flowering plant, native to the Mediterranean Basin, Mediterranean region, Central Europe, and southwestern Asia, from Morocco and Portugal north to southern Germany and east to northern ...

'', and ''

Zea mays Maize (; ''Zea mays''), also known as corn in North American English, is a tall stout Poaceae, grass that produces cereal grain. It was domesticated by indigenous peoples of Mexico, indigenous peoples in southern Mexico about 9,000 years ago ...

'' The purpose of the BioMarts in Ensembl Genomes is to allow the user to mine and download tables containing all the genes for a single species, genes in a specific region of a chromosome or genes on one region of a chromosome associated with an InterPro domain. The BioMarts also include filters to refine the data to be extracted and the attributes (Variant ID, Chromosome name, Ensembl ID, location, etc.) that will appear in the final table file can be selected by the user. The BioMarts can be accessed online in each corresponding domain of Ensembl Genomes or the source code can be installed in UNIX environment from the BioMart

git Git () is a distributed version control system that tracks versions of files. It is often used to control source code by programmers who are developing software collaboratively. Design goals of Git include speed, data integrity, and suppor ...

repository

BLAST

A BLAST interface is provided to allow users to search for

protein sequences Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...

against the Ensembl Genomes. It can be accessed by the header, located on top of all Ensembl Genome pages, titled BLAST. The BLAST search can be configured to search against individual species or collections of species (maximum of 25). There is a taxonomic browser to allow the selection of taxonomically related species.

Sequence Search

Ensembl Genomes provides a second sequence search tool, that uses an algorithm based on Exonerate, that is provided by

European Nucleotide Archive The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated nucleic acid sequence, DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of Genome p ...

. This tool can be accessed by the header, located on top of all Ensembl Genome pages, titled Sequence Search. Users can then choose whether they would like Exonerate to search against all species in the Ensembl Genomes division or against all species in Ensembl Genomes. They can also choose the 'Maximum E-value', which will limit the results that appear to those with E-values below the maximum. Finally users can choose to use an alternative search mode by selecting 'Use spliced query'.

Variant Effect Predictor

The Variant Effect Predictor is one of the most used tools in Ensembl and Ensembl Genomes. It allows to explore and analyse what is the effect that the variants (SNPs, CNVs, indels or structural variations) have on a particular gene, sequence, protein, transcript or transcription factor. To use VEP, the users must input the location of their variants and the nucleotide variations to generate the following results: * Genes and transcripts affected by the variant * Location of the variants * How the variant affects the protein synthesis (e.g. generating a stop codon) *Comparison with other databases to find equal known variants There are two ways in which the users can access the VEP. The first form is online-based. In this page, the user generates an input by selection the following parameters: # Species to be compared. The default database for comparison is Ensembl Transcripts, but for some species, other sources can be selected. # Name for the uploaded data (this is optional, but it will make easier to identify the data if many VEP jobs have been performed) # Selection of the input format for the data. If an incorrect file format is selected, VEP will throw an error when running. # Fields for data upload. Users can upload data from their computers, from an URL-based location or by copying directly their contents into a text box. Data upload to VEP supports VCF, pileup, HGVS notations and a default format. The default format is a whitespace-separated file that contains the data in columns. The first five columns indicate the chromosome, start location, end location, allele (pair of alleles separated by a '/', with the reference allele first) and the strand (+ for forward or – for reverse). The sixth column is a variation identifier and it is optional. If it is left in blank, VEP will assign an identifier to in output file. VEP also provides additional identifier options to the users, extra options to complement the output and filtering. The filtering options allow features like removal of known variants from results, returning variants in exons only, and restriction of results to specific consequences of the variants. VEP users also have the possibility of viewing and manipulating all the jobs associated with their session by browsing the "Recent Tickets" tab. In this tab the users can view the status of their search (success, queued, running or failed) and save, delete or resubmit jobs. The second option to use VEP is by downloading the source code for its use in UNIX environments. All the features are equal between the online and script versions. VEP can also be used with online instances like Galaxy. When a VEP job is completed the output is a tabular file that contains the following columns: # Uploaded variation - as chromosome_start_alleles # Location - in standard coordinate format (chr:start or chr:start-end) # Allele - the variant allele used to calculate the consequence # Gene - Ensembl stable ID of affected gene # Feature - Ensembl stable ID of feature # Feature type - type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature. # Consequence - consequence type of this variation # Position in cDNA - relative position of base pair in cDNA sequence # Position in CDS - relative position of base pair in coding sequence # Position in protein - relative position of amino acid in protein # Amino acid change - only given if the variation affects the protein-coding sequence # Codon change - the alternative codons with the variant base in upper case # Co-located variation - known identifier of existing variation # Extra - this column contains extra information as key=value pairs separated by ";". Displays extra identifiers. VEP output

Other common output formats for VEP include

JSON JSON (JavaScript Object Notation, pronounced or ) is an open standard file format and electronic data interchange, data interchange format that uses Human-readable medium and data, human-readable text to store and transmit data objects consi ...

and VDF formats.

Programmatic data access

The Ensembl Genomes ESTinterface allows access to the data using your favourite programming language. You can also access data using the Perl API and Biomart.

Current species

Ensembl Genomes makes no attempt to include all possible genomes, rather the genomes that are included on the site are those that are deemed to be scientifically important. Each site contains the following number of species: *The bacterial division of Ensembl now contains all bacterial genomes that have been completely sequenced, annotated and submitted to the

International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It involves the following computerized databases: NIG's DNA Data Bank of Japan ( ...

(European Nucleotide Archive, GenBank and the DNA Database of Japan). The current dataset contains 31,332 genomes. *Ensembl Fungi contains 1502 genomes *Ensembl Metazoa contains 333 genomes for

invertebrate Invertebrates are animals that neither develop nor retain a vertebral column (commonly known as a ''spine'' or ''backbone''), which evolved from the notochord. It is a paraphyletic grouping including all animals excluding the chordata, chordate s ...

species. The main Ensembl site contains 324 genomes for

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 ...

species. *Ensembl Plants contains 153 genomes *Ensembl Protists contains 237 genomes

Collaborations

Ensembl Genomes continuously expands the annotation data through collaboration with other organisations involved in genome annotation projects and research. The following organisations are collaborators of Ensembl Genomes: * AllBio *Barley *

Culicoides sonorensis ''Culicoides'' is a genus of biting midges in the family (biology), family Ceratopogonidae. There are over 1000 species in the genus,Connelly, C. RBiting midges: ''Culicoides'' spp.Featured Creatures, Entomology and Nematology Department, Univers ...

* Gramene * INFRAVEC * Microme * PomBase * PhytoPath * transPLANT * Triticeae Genomics for Sustainable Agriculture * VectorBase * Wheat Rust Genomic Improvement *

WormBase WormBase is an online biological database about the biology and genome of the nematode model organism ''Caenorhabditis elegans'' and contains information about other related nematodes. WormBase is used by the ''C. elegans'' research community bo ...

WormBase ParaSite

External links

Ensembl Genomes

Ensembl Genomes Documentation

Ensembl

EBI Home Page

Ensembl Genomes Legal Notices

Biomart Homepage

References

{{Wellcome Trust Genetics databases Genetic engineering in the United Kingdom Genomics organizations Medical databases in the United Kingdom Medical genetics Science and technology in Cambridgeshire South Cambridgeshire District Wellcome Trust

Displaying genomic data

Tools

Adding Custom tracks to Ensembl Genomes

BioMart

BLAST

Sequence Search

Variant Effect Predictor

Programmatic data access

Current species

Collaborations

See also

External links

References