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HandWiki. Ensembl Genomes. Encyclopedia. Available online: https://encyclopedia.pub/entry/30176 (accessed on 24 September 2026).
HandWiki. Ensembl Genomes. Encyclopedia. Available at: https://encyclopedia.pub/entry/30176. Accessed September 24, 2026.
HandWiki. "Ensembl Genomes" Encyclopedia, https://encyclopedia.pub/entry/30176 (accessed September 24, 2026).
HandWiki. (2022, October 19). Ensembl Genomes. In Encyclopedia. https://encyclopedia.pub/entry/30176
HandWiki. "Ensembl Genomes." Encyclopedia. Web. 19 October, 2022.
Ensembl Genomes
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The content is sourced from: https://handwiki.org/wiki/Biology:Ensembl_Genomes

Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species. The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl 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, fungi, invertebrate metazoa, plants, and protists. For each of the domains, the Ensembl 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 Perl API, virtual machines 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 a "permissive Apache-style open-source" license, making it free for all users.

virtual machines mysql ensembl

References

  1. Kersey, P. J.; Staines, D. M.; Lawson, D.; Kulesha, E.; Derwent, P.; Humphrey, J. C.; Hughes, D. S. T.; Keenan, S. et al. (2011). "Ensembl Genomes: An integrative resource for genome-scale data from non-vertebrate species". Nucleic Acids Research 40 (Database issue): D91–D97. doi:10.1093/nar/gkr895. PMID 22067447.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3245118
  2. "Whole Genome". Ensembl Genomes. http://fungi.ensembl.org/Help/View?id=154. Retrieved 7 September 2014. 
  3. "Frequently Asked Questions". Ensembl Genomes. http://ensemblgenomes.org/node/30399. Retrieved 7 September 2014. 
  4. Spudich, G; Fernández-Suárez, X. M.; Birney, E (2007). "Genome browsing with Ensembl: A practical overview". Briefings in Functional Genomics and Proteomics 6 (3): 202–19. doi:10.1093/bfgp/elm025. PMID 17967807.  https://dx.doi.org/10.1093%2Fbfgp%2Felm025
  5. "Uploading your data to Ensembl". Ensembl Genomes. http://ensemblgenomes.org/info/access/using-your-own-data. Retrieved 9 September 2014. 
  6. "Coordinates for data location in Ensembl Genomes". Ensembl Genomes. http://plants.ensembl.org/info/website/upload/coords.html#bacclone. Retrieved 9 September 2014. 
  7. "Methods for data upload". Ensembl Genomes. http://plants.ensembl.org/info/website/upload/index.html#formats. Retrieved 9 September 2014. 
  8. "Supported data files". Ensembl Genomes. http://plants.ensembl.org/info/website/upload/index.html#formats. Retrieved 9 September 2014. 
  9. "Saving and Sharing data in Ensembl Genomes". Ensembl Genomes. http://plants.ensembl.org/info/website/upload/index.html#formats. 
  10. "Data Mining in Ensembl with Data Mining in Ensembl with BioMart". 2014. p. 2. http://asia.ensembl.org/info/website/tutorials/mining_with_biomart.pdf. Retrieved 11 September 2014. 
  11. "Ensembl Protists". Ensembl Genomes. http://protists.ensembl.org/biomart/martview/b5a124953d0d5abc16130408a00a0195. Retrieved 1 October 2019. 
  12. "Ensembl Fungi". Ensembl Genomes. http://fungi.ensembl.org/biomart/martview/5b1b1f7a1f6a2367f491c6b553f6aa60. Retrieved 1 October 2019. 
  13. "Ensembl Metazoa". Ensembl Genomes. http://metazoa.ensembl.org/biomart/martview/ef188d8b8765e906ca1f6267a836a3c1. Retrieved 1 October 2019. 
  14. "Ensembl Plants". Ensembl Genomes. http://plants.ensembl.org/biomart/martview/300ab140234f173a3bcd1f77fa14f251. Retrieved 1 October 2019. 
  15. "Data Mining in Ensembl with Data Mining in Ensembl with BioMart". 2014. p. 3. http://asia.ensembl.org/info/website/tutorials/mining_with_biomart.pdf. Retrieved 11 September 2014. 
  16. "BioMart 0.9.0 user manual". May 2014. p. 5. http://www.biomart.org/other/biomart_0.9_0_documentation.pdf. Retrieved 11 September 2014. 
  17. "Frequently Asked Questions". Ensembl Genomes. http://ensemblgenomes.org/node/32859l. Retrieved 11 September 2014. 
  18. "Variant Effect Predictor". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/index.html. Retrieved 11 September 2014. 
  19. "Variant Effect Predictor results overview". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/index.html. Retrieved 11 September 2014. 
  20. "Data input to VEP". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/online/input.html#ident. Retrieved 11 September 2014. 
  21. "VEP supported file formats". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/vep_formats.html. Retrieved 11 September 2014. 
  22. "VEP default file". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/vep_formats.html. Retrieved 11 September 2014. 
  23. "VEP options and extras". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/online/input.html#ident. Retrieved 11 September 2014. 
  24. "VEP filtering". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/online/input.html#ident. Retrieved 11 September 2014. 
  25. "VEP jobs". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/online/input.html#ident. Retrieved 11 September 2014. 
  26. "VEP script download". Ensembl. http://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows. Retrieved 11 September 2014. 
  27. "VEP Output". Ensembl Genomes. http://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows. Retrieved 11 September 2014. 
  28. "VEP Output formats". Ensembl Genomes. http://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows. Retrieved 11 September 2014. 
  29. "Virtual Machines". Ensembl Genomes. http://ensemblgenomes.org/info/access/virtual_machine. Retrieved 11 September 2014. 
  30. "Species List". Ensembl Genomes. http://bacteria.ensembl.org/species.html. Retrieved 1 October 2019. 
  31. "Species List". Ensembl Genomes. http://fungi.ensembl.org/species.html. Retrieved 1 October 2019. 
  32. "Species List". Ensembl Genomes. http://metazoa.ensembl.org/species.html. Retrieved 1 October 2019. 
  33. "Species List". Ensembl Genomes. http://asia.ensembl.org/info/about/species.html. Retrieved 1 October 2019. 
  34. "Species List". Ensembl Genomes. https://plants.ensembl.org/species.html. Retrieved 1 October 2019. 
  35. "Species List". Ensembl Genomes. http://protists.ensembl.org/species.html. Retrieved 1 October 2019. 
  36. "Collaborators - Ensembl Genomes". Ensembl Genomes. http://ensemblgenomes.org/info/about/collaborations. Retrieved 3 September 2014. 
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