Nucleic Acids Research, 2005, Vol. 33, Database issue D447-D453
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
Ensembl 2005
Wellcome Trust Sanger Institute and 1 European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
* To whom correspondence should be addressed. Tel: +44 1223 494420; Fax: +44 1223 494470; Email: birney{at}ebi.ac.uk
Received October 6, 2004; Revised and Accepted November 1, 2004
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.© 2005, the authors
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J. H. Christiansen, Y. Yang, S. Venkataraman, L. Richardson, P. Stevenson, N. Burton, R. A. Baldock, and D. R. Davidson EMAGE: a spatial database of gene expression patterns during mouse embryo development Nucleic Acids Res., January 1, 2006; 34(suppl_1): D637 - D641. [Abstract] [Full Text] [PDF]
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A. S. Nord, P. J. Chang, B. R. Conklin, A. V. Cox, C. A. Harper, G. G. Hicks, C. C. Huang, S. J. Johns, M. Kawamoto, S. Liu, et al. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse Nucleic Acids Res., January 1, 2006; 34(suppl_1): D642 - D648. [Abstract] [Full Text] [PDF]
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F. Desiere, E. W. Deutsch, N. L. King, A. I. Nesvizhskii, P. Mallick, J. Eng, S. Chen, J. Eddes, S. N. Loevenich, and R. Aebersold The PeptideAtlas project Nucleic Acids Res., January 1, 2006; 34(suppl_1): D655 - D658. [Abstract] [Full Text] [PDF]
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F. Pattyn, P. Robbrecht, A. De Paepe, F. Speleman, and J. Vandesompele RTPrimerDB: the real-time PCR primer and probe database, major update 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D684 - D688. [Abstract] [Full Text] [PDF]
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P. Jaiswal, J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens-Clark, L. Ren, C. Liang, W. Zhao, K. Ratnapu, et al. Gramene: a bird's eye view of cereal genomes Nucleic Acids Res., January 1, 2006; 34(suppl_1): D717 - D723. [Abstract] [Full Text] [PDF]
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J. Lazar, C. Moreno, H. J. Jacob, and A. E. Kwitek Impact of genomics on research in the rat Genome Res., December 1, 2005; 15(12): 1717 - 1728. [Abstract] [Full Text] [PDF]
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P. F.R. Little Structure and function of the human genome Genome Res., December 1, 2005; 15(12): 1759 - 1766. [Abstract] [Full Text] [PDF]
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C. Webber and C. P. Ponting Hotspots of mutation and breakage in dog and human chromosomes Genome Res., December 1, 2005; 15(12): 1787 - 1797. [Abstract] [Full Text] [PDF]
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M. Dai, P. Wang, A. D. Boyd, G. Kostov, B. Athey, E. G. Jones, W. E. Bunney, R. M. Myers, T. P. Speed, H. Akil, et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucleic Acids Res., November 10, 2005; 33(20): e175 - e175. [Abstract] [Full Text] [PDF]
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M. Carter, X. Chen, B. Slowinska, S. Minnerath, S. Glickstein, L. Shi, F. Campagne, H. Weinstein, and M. E. Ross Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6 PNAS, September 6, 2005; 102(36): 12843 - 12848. [Abstract] [Full Text] [PDF]
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R. A. George, R. V. Spriggs, G. J. Bartlett, A. Gutteridge, M. W. MacArthur, C. T. Porter, B. Al-Lazikani, J. M. Thornton, and M. B. Swindells Inaugural Article: Effective function annotation through catalytic residue conservation PNAS, August 30, 2005; 102(35): 12299 - 12304. [Abstract] [Full Text] [PDF]
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S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma, and W. Huber BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis Bioinformatics, August 15, 2005; 21(16): 3439 - 3440. [Abstract] [Full Text] [PDF]
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M. Novatchkova, M. Wildpaner, D. Schweizer, and F. Eisenhaber PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets Nucleic Acids Res., July 1, 2005; 33(suppl_2): W121 - W125. [Abstract] [Full Text] [PDF]
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S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron SVC: structured visualization of evolutionary sequence conservation Nucleic Acids Res., July 1, 2005; 33(suppl_2): W271 - W273. [Abstract] [Full Text] [PDF]
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E. Berezikov, V. Guryev, and E. Cuppen CONREAL web server: identification and visualization of conserved transcription factor binding sites Nucleic Acids Res., July 1, 2005; 33(suppl_2): W447 - W450. [Abstract] [Full Text] [PDF]
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P. I. Olason Integrating protein annotation resources through the Distributed Annotation System Nucleic Acids Res., July 1, 2005; 33(suppl_2): W468 - W470. [Abstract] [Full Text] [PDF]
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N. Kim, D. Lim, S. Lee, and H. Kim ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs Nucleic Acids Res., July 1, 2005; 33(suppl_2): W681 - W685. [Abstract] [Full Text] [PDF]
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