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.<ref>{{cite PMID|19033362|noedit}}</ref> The main objective of the Ensembl Genomes database is to complement the main Ensembl
.<ref>{{cite PMID|19033362|noedit}}</ref> 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]], [[fungi]], invertebrate [[metazoa]], [[plant]]s, and [[protist]]s.<ref>{{cite web|title=About Ensembl Genomes|url=http://ensemblgenomes.org/info/about|website=http://ensemblgenomes.org/info/about|publisher=Ensembl|accessdate=2 September 2014}}</ref> For each of the domains, the [[Ensembl]] tools are available for manipulation, analysis and visualization of genome data.
database by introducing five additional web pages to include genome data for [[bacteria]], [[fungi]], invertebrate [[metazoa]], [[plant]]s, and [[protist]]s.<ref>{{cite web|title=About Ensembl Genomes|url=http://ensemblgenomes.org/info/about|website=http://ensemblgenomes.org/info/about|publisher=Ensembl|accessdate=2 September 2014}}</ref> For each of the domains, the [[Ensembl]] tools are available for manipulation, analysis and visualization of genome data.

Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public in order to exploit most of the data analysis and mining capabilities Ensembl technologies<ref>{{cite journal|last1=Kinsella|first1=Rhoda J.|last2=Kähäri|first2=Andreas|last3=Syed|first3=Haider|last4=Zamora|first4=Jorge|last5=Proctor|first5=Glenn|last6=Spudich|first6=Giulietta|last7=Almeida-King|first7=Jeff|last8=Staines|first8=Daniel|last9=Derwent|first9=Paul|last10=Kerhournou|first10=Arnaud|last11=Kersey|first11=Paul|last12=Flicek|first12=Paul|title=Ensembl BioMarts: a hub for data retrieval across taxonomic space|journal=Database|date=2011|volume=2011|issue=2011|page=2|pages=9|url=http://www.ncbi.nlm.nih.gov/pubmed/21785142|accessdate=3 September 2014}}</ref>.



== Using Ensembl Genomes ==
== Using Ensembl Genomes ==

Revision as of 11:33, 9 September 2014

Ensembl Genomes
Content
DescriptionAn integrative resource for genome-scale data from non-vertebrate species.
Data types
captured		Genomic database
Organismspan
Contact
Research centerEuropean Bioinformatics Institute
Primary citationKersey & al. (2012)[1]
Release date2009
Access
Websitehttp://ensemblgenomes.org/
Miscellaneous
Data release
frequency		4/5 times per year
VersionRelease 23 (July 2013)

Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species .[1] The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl technology .[2] 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, fungi, invertebrate metazoa, plants, and protists.[3] For each of the domains, the Ensembl tools are available for manipulation, analysis and visualization of genome data.

Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public in order to exploit most of the data analysis and mining capabilities Ensembl technologies[4].


Using Ensembl Genomes

File:Anopheles gambiae Ensembl Genomes.png
Result page for a species search using Ensembl Genomes

Ensembl Genome allows to find specific gene or DNA sequence data or whole karyotypes. Genes can be accessed by name, gene symbol, accession number or Variant ID. Genome search by species is also possible using the corresponding binomial nomenclature. Searching for a particular species using Ensembl Genomes redirects to a new page in which all the tools and information available for the species are shown. In general, each result page contains the following sections:

  • Genome Assembly
  • Comparative Genomics
  • Gene annotation
  • Variation

A karyotype is available for some species in Ensembl Genomes. [5] 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.[6] This will open the ‘Location’ Tab.

In the 'Location' tab, users can browse genes, variations, sequence conservation, and other types of annotation along the genome. [7] 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. [8] Data from the following categories can be easily added or removed from this 'Location' tab view: 'Sequence and assembly', 'Genes and transcripts', 'mRNA and protein alignments', 'Other DNA alignments', 'Germline variation', 'Comparative genomics', among others. [9] Users can also change the display options such as the width.[10] A further option allows users to reset the configuration back to the default settings. [11]

More specific information about a select gene 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 and homology information.[1] 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. [1]


Current 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 (European Nucleotide Archive, GenBank and the DNA Database of Japan).[12] The current dataset contains 15,270 genomes.[13]
  • Ensembl Fungi contains 52 genomes [14]
  • Ensembl Metazoa contains 54 genomes [15]
  • Ensembl Plants contains 38 genomes [16]
  • Ensembl Protists contains 32 genomes [17]

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:[18]

See also

References

  1. ^ a b c d Template:Cite PMID Cite error: The named reference "kersey" was defined multiple times with different content (see the help page).
  2. ^ Template:Cite PMID
  3. ^ "About Ensembl Genomes". http://ensemblgenomes.org/info/about. Ensembl. Retrieved 2 September 2014. {{cite web}}: External link in |website= (help)
  4. ^ Kinsella, Rhoda J.; Kähäri, Andreas; Syed, Haider; Zamora, Jorge; Proctor, Glenn; Spudich, Giulietta; Almeida-King, Jeff; Staines, Daniel; Derwent, Paul; Kerhournou, Arnaud; Kersey, Paul; Flicek, Paul (2011). "Ensembl BioMarts: a hub for data retrieval across taxonomic space". Database. 2011 (2011): 2. Retrieved 3 September 2014. {{cite journal}}: More than one of |pages= and |page= specified (help)
  5. ^ "Whole Genome". Ensembl Genomes. Retrieved 7 September 2014.
  6. ^ "Whole Genome". Ensembl Genomes. Retrieved 7 September 2014.
  7. ^ "Frequently Asked Questions". Ensembl Genomes. Retrieved 7 September 2014.
  8. ^ "Frequently Asked Questions". Ensembl Genomes. Retrieved 7 September 2014.
  9. ^ "Frequently Asked Questions". Ensembl Genomes. Retrieved 7 September 2014.
  10. ^ "Frequently Asked Questions". Ensembl Genomes. Retrieved 7 September 2014.
  11. ^ "Frequently Asked Questions". Ensembl Genomes. Retrieved 7 September 2014.
  12. ^ Template:Cite PMID
  13. ^ "Ensembl Bacteria". Ensembl Genomes. Retrieved 6 September 2014.
  14. ^ "Ensembl Fungi Species". Ensembl Genomes. Retrieved 6 September 2014.
  15. ^ "Ensembl Metazoa Species". Ensembl Genomes. Retrieved 6 September 2014.
  16. ^ "Ensembl Plants Species". Ensembl Genomes. Retrieved 6 September 2014.
  17. ^ "Ensembl Protists Species". Ensembl Genomes. Retrieved 6 September 2014.
  18. ^ "Collaborators - Ensembl Genomes". http://ensemblgenomes.org/info/about/collaborations. Ensembl Genomes. Retrieved 3 September 2014. {{cite web}}: External link in |website= (help)
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