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A [[karyotype]] is available for some species in Ensembl Genomes. <ref>{{cite web |url=http://fungi.ensembl.org/Help/View?id=154 |title = Whole Genome |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> 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.<ref>{{cite web |url=http://fungi.ensembl.org/Help/View?id=154 |title = Whole Genome |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> This will open the ‘Location’ Tab.
A [[karyotype]] is available for some species in Ensembl Genomes. <ref>{{cite web |url=http://fungi.ensembl.org/Help/View?id=154 |title = Whole Genome |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> 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.<ref>{{cite web |url=http://fungi.ensembl.org/Help/View?id=154 |title = Whole Genome |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> This will open the ‘Location’ Tab.


In the 'Location' tab, users can browse [[genes]], variations, [[sequence conservation]], and other types of [[DNA annotation|annotation]] along the [[genome]]. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> 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. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> Data from the following categories can be easily added or removed from this 'Location' tab view: '[[Sequence]] and [[Sequence assembly|assembly]]', '[[Genes]] and [[transcripts]]', '[[mRNA]] and [[protein]] alignments', 'Other [[DNA]] [[Sequence alignment|alignments]]', '[[Germline]] variation', '[[Comparative genomics]]', among others. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> Users can also change the display options such as the width.<ref> {{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> A further option allows users to reset the configuration back to the default settings. <ref> {{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref>
In the 'Location' tab, users can browse [[genes]], variations, [[sequence conservation]], and other types of [[DNA annotation|annotation]] along the [[genome]]. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> 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. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> Data from the following categories can be easily added or removed from this 'Location' tab view: '[[Sequence]] and [[Sequence assembly|assembly]]', '[[Genes]] and [[Transcription (genetics)|transcript]]s', '[[mRNA]] and [[protein]] alignments', 'Other [[DNA]] [[Sequence alignment|alignments]]', '[[Germline]] variation', '[[Comparative genomics]]', among others. <ref>{{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> Users can also change the display options such as the width.<ref> {{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref> A further option allows users to reset the configuration back to the default settings. <ref> {{cite web |url=http://ensemblgenomes.org/node/30399 |title = Frequently Asked Questions |publisher=Ensembl Genomes|accessdate=7 September 2014}}</ref>


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.<ref name="kersey">{{cite PMID|17967807|noedit}}</ref> This information can be accessed via the menu on the left-hand side.
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.<ref name="kersey">{{cite PMID|17967807|noedit}}</ref> This information can be accessed via the menu on the left-hand side.

Revision as of 14:39, 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[4], allowing researchers and organisations to exploit most of the data analysis and mining capabilities of Ensembl technology.


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]


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 to Ensembl Genomes or to modify data that has been previously uploaded[12]. 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[13]. The following methods can be used to upload a data file to any Ensembl Genomes page[14]:

  1. Files smaller than 5 MB can be either uploaded directly from any computer or from a web location (URL) to the Ensembl servers.
  2. Lager files can only be uploaded from web locations (URL).
  3. BAM files can only be uploaded using the URL-based approach. The index file (.bam.bai) should be located in the same webserver.
  4. A Distributed Annotation System source can be attached from web locations.

The following file types are supported by Ensembl Genomes[15]:

Visualisation of a custom track labelled "Reads" in 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 URL assigned to it[16]. Users are also allowed to delete their custom tracks from Ensembl Genomes.


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).[17] The current dataset contains 15,270 genomes.[18]
  • Ensembl Fungi contains 52 genomes [19]
  • Ensembl Metazoa contains 54 genomes [20]
  • Ensembl Plants contains 38 genomes [21]
  • Ensembl Protists contains 32 genomes [22]

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:[23]

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.
  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. ^ "Uploading your data to Ensembl". Ensembl Genomes. Ensembl Genomes. Retrieved 9 September 2014.
  13. ^ "Coordinates for data location in Ensembl Genomes". Ensembl Genomes. Ensembl Genomes. Retrieved 9 September 2014.
  14. ^ "Methods for data upload". Ensembl Plants. Ensembl Genomes. Retrieved 9 September 2014.
  15. ^ "Supported data files". Ensembl Plants. Ensembl Genomes. Retrieved 9 September 2014.
  16. ^ "Saving and Sharing data in Ensembl Genomes". Ensembl Plants. Ensembl Genomes.
  17. ^ Template:Cite PMID
  18. ^ "Ensembl Bacteria". Ensembl Genomes. Retrieved 6 September 2014.
  19. ^ "Ensembl Fungi Species". Ensembl Genomes. Retrieved 6 September 2014.
  20. ^ "Ensembl Metazoa Species". Ensembl Genomes. Retrieved 6 September 2014.
  21. ^ "Ensembl Plants Species". Ensembl Genomes. Retrieved 6 September 2014.
  22. ^ "Ensembl Protists Species". Ensembl Genomes. Retrieved 6 September 2014.
  23. ^ "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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