Ensembl 2004 - PubMed (original) (raw)

. 2004 Jan 1;32(Database issue):D468-70.

doi: 10.1093/nar/gkh038.

D Andrews, P Bevan, M Caccamo, G Cameron, Y Chen, L Clarke, G Coates, T Cox, J Cuff, V Curwen, T Cutts, T Down, R Durbin, E Eyras, X M Fernandez-Suarez, P Gane, B Gibbins, J Gilbert, M Hammond, H Hotz, V Iyer, A Kahari, K Jekosch, A Kasprzyk, D Keefe, S Keenan, H Lehvaslaiho, G McVicker, C Melsopp, P Meidl, E Mongin, R Pettett, S Potter, G Proctor, M Rae, S Searle, G Slater, D Smedley, J Smith, W Spooner, A Stabenau, J Stalker, R Storey, A Ureta-Vidal, C Woodwark, M Clamp, T Hubbard

Affiliations

• PMID: 14681459
• PMCID: PMC308772
• DOI: 10.1093/nar/gkh038

Ensembl 2004

E Birney et al. Nucleic Acids Res. 2004.

Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

PubMed Disclaimer

Similar articles

• Ensembl 2002: accommodating comparative genomics.
  Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. Clamp M, et al. Nucleic Acids Res. 2003 Jan 1;31(1):38-42. doi: 10.1093/nar/gkg083. Nucleic Acids Res. 2003. PMID: 12519943 Free PMC article.
• The Ensembl genome database project.
  Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M. Hubbard T, et al. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. doi: 10.1093/nar/30.1.38. Nucleic Acids Res. 2002. PMID: 11752248 Free PMC article.
• Genome information resources - developments at Ensembl.
  Hammond MP, Birney E. Hammond MP, et al. Trends Genet. 2004 Jun;20(6):268-72. doi: 10.1016/j.tig.2004.04.002. Trends Genet. 2004. PMID: 15145580 Review.
• An overview of Ensembl.
  Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M. Birney E, et al. Genome Res. 2004 May;14(5):925-8. doi: 10.1101/gr.1860604. Epub 2004 Apr 12. Genome Res. 2004. PMID: 15078858 Free PMC article. Review.
• Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.
  Sand O, Thomas-Chollier M, van Helden J. Sand O, et al. Bioinformatics. 2009 Oct 15;25(20):2739-40. doi: 10.1093/bioinformatics/btp519. Epub 2009 Aug 31. Bioinformatics. 2009. PMID: 19720677

Cited by

• Reactome graph database: Efficient access to complex pathway data.
  Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. Fabregat A, et al. PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan. PLoS Comput Biol. 2018. PMID: 29377902 Free PMC article.
• Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients.
  Erives AJ, Fassler JS. Erives AJ, et al. PLoS One. 2015 Feb 24;10(2):e0117192. doi: 10.1371/journal.pone.0117192. eCollection 2015. PLoS One. 2015. PMID: 25710177 Free PMC article.
• A novel splice variant of XIAP-associated factor 1 (XAF1) is expressed in peripheral blood containing gastric cancer-derived circulating tumor cells.
  Hatakeyama K, Yamakawa Y, Fukuda Y, Ohshima K, Wakabayashi-Nakao K, Sakura N, Tanizawa Y, Kinugasa Y, Yamaguchi K, Terashima M, Mochizuki T. Hatakeyama K, et al. Gastric Cancer. 2015 Oct;18(4):751-61. doi: 10.1007/s10120-014-0426-3. Epub 2014 Sep 13. Gastric Cancer. 2015. PMID: 25216542
• Discovery of a metabolic alternative to the classical mevalonate pathway.
  Dellas N, Thomas ST, Manning G, Noel JP. Dellas N, et al. Elife. 2013 Dec 10;2:e00672. doi: 10.7554/eLife.00672. Elife. 2013. PMID: 24327557 Free PMC article.
• Robust demographic inference from genomic and SNP data.
  Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M. Excoffier L, et al. PLoS Genet. 2013 Oct;9(10):e1003905. doi: 10.1371/journal.pgen.1003905. Epub 2013 Oct 24. PLoS Genet. 2013. PMID: 24204310 Free PMC article.

References

1. 1. Waterston R.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562. - PubMed
2. 1. Holt R.A., Subramanian,G.M., Halpern,A., Sutton,G.G., Charlab,R., Nusskern,D.R., Wincker,P., Clark,A.G., Ribeiro,J.M., Wides,R. et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298, 129–149. - PubMed
3. 1. Birney E., Clamp,M.E. and Hubbard,T.J. (2002) Databases and tools for browsing genomes. Annu. Rev. Genom. Hum. Genet., 3, 293–310. - PubMed
4. 1. Lewis S.E., Searle,S.M., Harris,N., Gibson,M., Lyer,V., Richter,J., Wiel,C., Bayraktaroglir,L., Birney,E., Crosby,M.A. et al. (2002) Apollo: a sequence annotation editor. Genome Biol., 3, RESEARCH0082. - PMC - PubMed
5. 1. Hoon S., Ratnapu,K.K., Chia,J.M., Kumarasamy,B., Juguang,X., Clamp,M., Stabenau,A., Potter,S., Clarke,L. and Stupka,E. (2003) Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res., 13, 1904–1915. - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • Ovid Technologies, Inc.
  • PubMed Central
  • Silverchair Information Systems

• Research Materials

  • NCI CPTC Antibody Characterization Program