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Nucleic Acids Research, 2002, Vol. 30, No. 1 38-41
© 2002 Oxford University Press

The Ensembl genome database project

T. Hubbard, D. Barker, E. Birney1,*, G. Cameron1, Y. Chen1, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond1, L. Huminiecki1, A. Kasprzyk1, H. Lehvaslaiho1, P. Lijnzaad1, C. Melsopp1, E. Mongin1, R. Pettett, M. Pocock, S. Potter, A. Rust1, E. Schmidt1, S. Searle, G. Slater1, J. Smith, W. Spooner, A. Stabenau1, J. Stalker, E. Stupka1, A. Ureta-Vidal1, I. Vastrik1 and M. Clamp

The Wellcome Trust Sanger Institute and 1European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

* To whom correspondence should be addressed. Tel: +44 1223 494420; Fax: +44 1223 494468; Email: birney{at}ebi.ac.uk


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M. Liu, H. Walch, S. Wu, and A. Grigoriev
Significant expansion of exon-bordering protein domains during animal proteome evolution
Nucleic Acids Res., January 7, 2005; 33(1): 95 - 105.
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 IOVSHome page
V. L. Ramprasad, A. Thool, S. Murugan, D. Nancarrow, P. Vyas, S. K. Rao, A. Vidhya, K. Ravishankar, and G. Kumaramanickavel
Truncating Mutation in the NHS Gene: Phenotypic Heterogeneity of Nance-Horan Syndrome in an Asian Indian Family
Invest. Ophthalmol. Vis. Sci., January 1, 2005; 46(1): 17 - 23.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
L. Florea, V. Di Francesco, J. Miller, R. Turner, A. Yao, M. Harris, B. Walenz, C. Mobarry, G. V. Merkulov, R. Charlab, et al.
Gene and alternative splicing annotation with AIR
Genome Res., January 1, 2005; 15(1): 54 - 66.
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 Nucleic Acids ResHome page
P. Lu, D. Szafron, R. Greiner, D. S. Wishart, A. Fyshe, B. Pearcy, B. Poulin, R. Eisner, D. Ngo, and N. Lamb
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D147 - D153.
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 Nucleic Acids ResHome page
A. Bairoch, R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, et al.
The Universal Protein Resource (UniProt)
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D154 - D159.
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 Nucleic Acids ResHome page
N. de la Cruz, S. Bromberg, D. Pasko, M. Shimoyama, S. Twigger, J. Chen, C.-F. Chen, C. Fan, C. Foote, G. R. Gopinath, et al.
The Rat Genome Database (RGD): developments towards a phenome database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D485 - D491.
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 ScienceHome page
P. Bertone, V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, et al.
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
Science, December 24, 2004; 306(5705): 2242 - 2246.
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 IOVSHome page
S. Aijaz, B. J. Clark, K. Williamson, V. van Heyningen, D. Morrison, D. FitzPatrick, R. Collin, N. Ragge, A. Christoforou, A. Brown, et al.
Absence of SIX6 Mutations in Microphthalmia, Anophthalmia, and Coloboma
Invest. Ophthalmol. Vis. Sci., November 1, 2004; 45(11): 3871 - 3876.
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Y. Tamimi, M. Lines, M. Coca-Prados, and M. A. Walter
Identification of Target Genes Regulated by FOXC1 Using Nickel Agarose-Based Chromatin Enrichment
Invest. Ophthalmol. Vis. Sci., November 1, 2004; 45(11): 3904 - 3913.
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 RNAHome page
M. REHMSMEIER, P. STEFFEN, M. HOCHSMANN, and R. GIEGERICH
Fast and effective prediction of microRNA/target duplexes
RNA, October 20, 2004; 10(10): 1507 - 1517.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
L. Huminiecki and K. H. Wolfe
Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse
Genome Res., October 1, 2004; 14(10a): 1870 - 1879.
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 Genome ResHome page
A. Baross, Y. S.N. Butterfield, S. M. Coughlin, T. Zeng, M. Griffith, O. L. Griffith, A. S. Petrescu, D. E. Smailus, J. Khattra, H. L. McDonald, et al.
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
Genome Res., October 1, 2004; 14(10b): 2083 - 2092.
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 J. Biol. Chem.Home page
J. R. Beckley, B. U. Pauli, and R. C. Elble
Re-expression of Detachment-inducible Chloride Channel mCLCA5 Suppresses Growth of Metastatic Breast Cancer Cells
J. Biol. Chem., October 1, 2004; 279(40): 41634 - 41641.
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 Genome ResHome page
A.-M. Mallon, L. Wilming, J. Weekes, J. G.R. Gilbert, J. Ashurst, S. Peyrefitte, L. Matthews, M. Cadman, R. McKeone, C. A. Sellick, et al.
Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
Genome Res., October 1, 2004; 14(10a): 1888 - 1901.
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 Nucleic Acids ResHome page
J. Leipzig, P. Pevzner, and S. Heber
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome
Nucleic Acids Res., August 3, 2004; 32(13): 3977 - 3983.
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 BloodHome page
W. Wagner, A. Ansorge, U. Wirkner, V. Eckstein, C. Schwager, J. Blake, K. Miesala, J. Selig, R. Saffrich, W. Ansorge, et al.
Molecular evidence for stem cell function of the slow-dividing fraction among human hematopoietic progenitor cells by genome-wide analysis
Blood, August 1, 2004; 104(3): 675 - 686.
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 Genome ResHome page
M. R. Weil, P. Widlak, J. D. Minna, and H. R. Garner
Global Survey of Chromatin Accessibility Using DNA Microarrays
Genome Res., July 1, 2004; 14(7): 1374 - 1381.
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 Nucleic Acids ResHome page
N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen, and R. Lopez
Public web-based services from the European Bioinformatics Institute
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W3 - W9.
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 Nucleic Acids ResHome page
S. Weckx, P. De Rijk, C. Van Broeckhoven, and J. Del-Favero
SNPbox: web-based high-throughput primer design from gene to genome
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W170 - W172.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
N. Kim, S. Shin, and S. Lee
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W181 - W186.
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 Nucleic Acids ResHome page
M. Kankainen and L. Holm
POBO, transcription factor binding site verification with bootstrapping
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W222 - W229.
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 Nucleic Acids ResHome page
I. Ovcharenko, M. A. Nobrega, G. G. Loots, and L. Stubbs
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W280 - W286.
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 Nucleic Acids ResHome page
D. Szafron, P. Lu, R. Greiner, D. S. Wishart, B. Poulin, R. Eisner, Z. Lu, J. Anvik, C. Macdonell, A. Fyshe, et al.
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W365 - W371.
[Abstract] [Full Text] [PDF]


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