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 Well ...
, 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 (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
,
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, invertebrate
metazoa
Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in ...
,
plant
Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclud ...
s, and
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
s. For each of the domains, 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 ...
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
In the fields of molecular biology and genetics, 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 ge ...
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 in the margin of book pages. For anno ...
(e.g.
genes
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
,
SNP loci), sequence patterns (e.g. repeats) and experimental data (e.g. sequences and external sequence features mapped onto the
genome
In the fields of molecular biology and genetics, 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 ge ...
).
Graphical views are available for varying levels of resolution from an entire
karyotype
A karyotype is the general appearance of the complete set of metaphase 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 disce ...
, 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 sequen ...
. Information for a
genome
In the fields of molecular biology and genetics, 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 ge ...
is spread over four tabs, a species page, a ‘Location’ tab, a ‘
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
’ 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
genome
In the fields of molecular biology and genetics, 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 ge ...
, the graphical interface and some of the tools available.
A
karyotype
A karyotype is the general appearance of the complete set of metaphase 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 disce ...
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
genes
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
, 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
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 in the margin of book pages. For anno ...
along the
genome
In the fields of molecular biology and genetics, 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 ge ...
.
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 calle ...
and
assembly
Assembly may refer to:
Organisations and meetings
* Deliberative assembly, a gathering of members who use parliamentary procedure for making decisions
* General assembly, an official meeting of the members of an organization or of their representa ...
', '
Genes
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
alignments', 'Other
DNA alignments', '
Germline
In biology and genetics, the germline is the population of a multicellular organism's cells that pass on their genetic material to the progeny (offspring). In other words, they are the cells that form the egg, sperm and the fertilised egg. They ...
variation', '
Comparative genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...
', 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 (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
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 long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
and
homology
Homology may refer to:
Sciences
Biology
*Homology (biology), any characteristic of biological organisms that is derived from a common ancestor
* Sequence homology, biological homology between DNA, RNA, or protein sequences
*Homologous chrom ...
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
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. Although the BioMart software ...
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 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 called "pot ...
'' and ''
Phaeodactylum tricornutum
''Phaeodactylum tricornutum'' is a diatom. It is the only species in the genus ''Phaeodactylum''. Unlike other diatoms, ''P. tricornutum'' can exist in different morphotypes (wikt:Special:Search/fusiform, fusiform, triradiate, and oval) and chang ...
''
* 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 dolla ...
'', ''
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
Stem rust, also known as cereal rust, black rust, red rust or red dust, is caused by the fungus ''Puccinia graminis'', which causes significant disease in cereal crops. Crop species that are affected by the disease include bread wheat, durum whe ...
'', ''
Verticillium dahliae
''Verticillium dahliae'' is a fungal plant pathogen. It causes verticillium wilt in many plant species, causing leaves to curl and discolor. It may cause death in some plants. Over 400 plant species are affected by ''Verticillium'' complex.
...
'', ''
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 d ...
'', and ''
Saccharomyces cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...
''
* Ensembl Metazoa BioMart: includes 78 species and variations for ''
Aedes aegypti
''Aedes aegypti'', the yellow fever mosquito, is a mosquito that can spread dengue fever, chikungunya, Zika fever, Mayaro and yellow fever viruses, and other disease agents. The mosquito can be recognized by black and white markings on its legs ...
'', ''
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 commonly known as the deer tick or black-legged tick (although some people reserve the latter term for ''Ixodes pacificus'', which is found on the west coast of the US), and in some parts of the US as the bear tick. It wa ...
''
* Ensembl Plants: includes 67 species and variations for ''
Arabidopsis thaliana
''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land.
A winter a ...
'', ''
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
Barley (''Hordeum vulgare''), a member of the grass family, is a major cereal grain grown in temperate climates globally. It was one of the first cultivated grains, particularly in Eurasia as early as 10,000 years ago. Globally 70% of barley pr ...
'', ''
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 ri ...
'', ''
Oryza glumipatula'',
''Oryoza sativa indica'',
''Oryza sativa japonica'', ''
Solanum lycopersicum
The tomato is the edible berry of the plant ''Solanum lycopersicum'', commonly known as the tomato plant. The species originated in western South America, Mexico, and Central America. The Mexican Nahuatl word gave rise to the Spanish word ...
'', ''
Sorghum bicolor
''Sorghum bicolor'', commonly called sorghum () and also known as great millet, broomcorn, guinea corn, durra, imphee, jowar, or milo, is a Poaceae, grass species cultivated for its grain, which is used for food for humans, animal feed, and ethan ...
'', ''
Triticum aestivum
Common wheat (''Triticum aestivum''), also known as bread wheat, is a cultivated wheat species. About 95% of wheat produced worldwide is common wheat; it is the most widely grown of all crops and the cereal with the highest monetary yield.
Ta ...
'', ''
Vitis vinifera
''Vitis vinifera'', the common grape vine, is a species of flowering plant, native to the Mediterranean region, Central Europe, and southwestern Asia, from Morocco and Portugal north to southern Germany and east to northern Iran. There are curre ...
'', and ''
Zea mays
Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. Th ...
''
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: tracking changes in any set of files, usually used for coordinating work among programmers collaboratively developing source code during software development. Its goals include speed, data in ...
repository
BLAST
A
BLAST
Blast or The Blast may refer to:
* Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film) ...
interface is provided to allow users to search for
DNA or
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
Blast or The Blast may refer to:
* Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film) ...
. The
BLAST
Blast or The Blast may refer to:
* Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film) ...
search can be configured to search against individual species or collections of species (maximum of 25). There is a
taxonomic
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
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 DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other m ...
.
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. I 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](https://upload.wikimedia.org/wikipedia/commons/b/b1/VEP_output.png)
Other common output formats for VEP include
JSON
JSON (JavaScript Object Notation, pronounced ; also ) is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other ser ...
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: DNA Data Bank of Japan (Japan ...
(European Nucleotide Archive, GenBank and the DNA Database of Japan).
The current dataset contains 44,048 genomes.
*Ensembl Fungi contains 1014 genomes
*Ensembl Metazoa contains 78 genomes for
invertebrate
Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordate ...
species. The main Ensembl site contains 236 genomes for
vertebrate
Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...
species.
*Ensembl Plants contains 67 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 Ceratopogonidae. There are over 1000 species in the genus,Connelly, C. RBiting midges: ''Culicoides'' spp.Featured Creatures, Entomology and Nematology Department, University of Florida IFA ...
*
Gramene
*
INFRAVEC
*
Microme
*
PomBase
PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase webs ...
*
PhytoPath
PhytoPath was a joint scientific project between the European Bioinformatics Institute and Rothamsted Research, running from January 2012 to May 30, 2017. The project aimed to enable the exploitation of the growing body of “-omics” data being ...
*
transPLANT
*
Triticeae Genomics for Sustainable Agriculture
*
VectorBase VectorBase is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Departm ...
*
Wheat Rust Genomic Improvement
*
WormBaseWormBase ParaSite
See also
*
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 ...
*
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 Well ...
*
BLAST
Blast or The Blast may refer to:
* Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film) ...
*
BLAT
*
WormBase
*
VectorBase VectorBase is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Departm ...
*
List of sequenced plant genomes
This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated and published. Unassembled genomes are not included, nor are organelle only sequences. For al ...
*
List of sequenced bacterial genomes
This list of sequenced eubacterial genomes contains most of the eubacteria known to have publicly available complete genome sequences. Most of these sequences have been placed in the International Nucleotide Sequence Database Collaboration, a publ ...
*
List of sequenced protist genomes
This list of sequenced protist genomes contains all the protist species known to have publicly available complete genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle only sequences. ...
*
List of sequenced fungi genomes
This list of sequenced fungi genomes contains all the fungal species known to have publicly available complete genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle only sequences.
...
*
List of sequenced archaeal genomes
This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences that have been assembled, annotated and deposited in public databases. ''Methanococcus jannaschii'' was the first archaeon ...
*
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. Methodologies used include sequence alignm ...
*
Structural variation Genomic structural variation is the variation in structure of an organism's chromosome. It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, ...
External links
Ensembl GenomesEnsembl Genomes DocumentationEnsemblEBI Home PageEnsembl Genomes Legal NoticesBiomart 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