Nucleic Acids Research, 2002, Vol. 30, No. 1 38-41
© 2002 Oxford University Press
The Ensembl genome database project
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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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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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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. [Abstract] [Full Text] [PDF]
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M. Kankainen and L. Holm POBO, transcription factor binding site verification with bootstrapping Nucleic Acids Res., July 1, 2004; 32(suppl_2): W222 - W229. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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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T. R. Pacheco, A. Q. Gomes, N. L. Barbosa-Morais, V. Benes, W. Ansorge, M. Wollerton, C. W. Smith, J. Valcarcel, and M. Carmo-Fonseca Diversity of Vertebrate Splicing Factor U2AF35: IDENTIFICATION OF ALTERNATIVELY SPLICED U2AF1 mRNAs J. Biol. Chem., June 25, 2004; 279(26): 27039 - 27049. [Abstract] [Full Text] [PDF]
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