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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Eddy and N. Maizels Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes Nucleic Acids Res., March 27, 2008; 36(4): 1321 - 1333. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Ansong, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith Proteogenomics: needs and roles to be filled by proteomics in genome annotation Brief Funct Genomic Proteomic, March 10, 2008; (2008) eln010v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Selman, S. Lingard, A. I. Choudhury, R. L. Batterham, M. Claret, M. Clements, F. Ramadani, K. Okkenhaug, E. Schuster, E. Blanc, et al. Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice FASEB J, March 1, 2008; 22(3): 807 - 818. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U. J. Pape, S. Rahmann, and M. Vingron Natural similarity measures between position frequency matrices with an application to clustering Bioinformatics, February 1, 2008; 24(3): 350 - 357. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Ek, M. Dictor, M. Jerkeman, K. Jirstrom, and C. A. K. Borrebaeck Nuclear expression of the non B-cell lineage Sox11 transcription factor identifies mantle cell lymphoma Blood, January 15, 2008; 111(2): 800 - 805. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Calabrese, A. C. Seila, G. W. Yeo, and P. A. Sharp RNA sequence analysis defines Dicer's role in mouse embryonic stem cells PNAS, November 13, 2007; 104(46): 18097 - 18102. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. L. Maeder, B. J. Polansky, B. E. Robson, and D. A. Eastman Phylogenetic Footprinting Analysis in the Upstream Regulatory Regions of the Drosophila Enhancer of split Genes Genetics, November 1, 2007; 177(3): 1377 - 1394. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. J.A. Frost and S. Engelhardt A Secretion Trap Screen in Yeast Identifies Protease Inhibitor 16 as a Novel Antihypertrophic Protein Secreted From the Heart Circulation, October 16, 2007; 116(16): 1768 - 1775. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Schneider, C. Dessimoz, and G. H. Gonnet OMA Browser Exploring orthologous relations across 352 complete genomes Bioinformatics, August 15, 2007; 23(16): 2180 - 2182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Wagner Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters Genetics, August 1, 2007; 176(4): 2451 - 2463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. de Ridder, J. Kool, A. Uren, J. Bot, L. Wessels, and M. Reinders Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes Bioinformatics, July 1, 2007; 23(13): i133 - i141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Mungall, D. B. Emmert, and The FlyBase Consortium A Chado case study: an ontology-based modular schema for representing genome-associated biological information Bioinformatics, July 1, 2007; 23(13): i337 - i346. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Sasidharan and C. Chothia The selection of acceptable protein mutations PNAS, June 12, 2007; 104(24): 10080 - 10085. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. E. Thurman, N. Day, W. S. Noble, and J. A. Stamatoyannopoulos Identification of higher-order functional domains in the human ENCODE regions Genome Res., June 1, 2007; 17(6): 917 - 927. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Osato, Y. Suzuki, K. Ikeo, and T. Gojobori Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice Genetics, June 1, 2007; 176(2): 1299 - 1306. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Panizzi, J. R. Jessen, I. A. Drummond, and L. Solnica-Krezel New functions for a vertebrate Rho guanine nucleotide exchange factor in ciliated epithelia Development, March 1, 2007; 134(5): 921 - 931. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Semon and K. H. Wolfe Rearrangement Rate following the Whole-Genome Duplication in Teleosts Mol. Biol. Evol., March 1, 2007; 24(3): 860 - 867. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting, P. Harrrison, and M. Gerstein Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation Nucleic Acids Res., January 12, 2007; 35(suppl_1): D55 - D60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Erwin, E. G. Jewell, C. G. Love, G. A. C. Lim, X. Li, R. Chapman, J. Batley, J. E. Stajich, E. Mongin, E. Stupka, et al. BASC: an integrated bioinformatics system for Brassica research Nucleic Acids Res., January 12, 2007; 35(suppl_1): D870 - D873. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Rissone, M. Monopoli, M. Beltrame, F. Bussolino, F. Cotelli, and M. Arese Comparative Genome Analysis of the Neurexin Gene Family in Danio rerio: Insights into Their Functions and Evolution Mol. Biol. Evol., January 1, 2007; 24(1): 236 - 252. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Seoighe, V. Nembaware, and K. Scheffler Maximum likelihood inference of imprinting and allele-specific expression from EST data Bioinformatics, December 15, 2006; 22(24): 3032 - 3039. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Mullins, L. J. Mullins, D. R. Dunbar, W. J. Brammar, K. W. Gross, and S. D. Morley Identification of a human ortholog of the mouse Dcpp gene locus, encoding a novel member of the CSP-1/Dcpp salivary protein family Physiol Genomics, December 13, 2006; 28(1): 129 - 140. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Notari, V. Baladron, J. D. Aroca-Aguilar, N. Balko, R. Heredia, C. Meyer, P. M. Notario, S. Saravanamuthu, M.-L. Nueda, F. Sanchez-Sanchez, et al. Identification of a Lipase-linked Cell Membrane Receptor for Pigment Epithelium-derived Factor J. Biol. Chem., December 8, 2006; 281(49): 38022 - 38037. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Crandall, D. M. Dunn, Y. Ma, R. M. Wooten, J. F. Zachary, J. H. Weis, R. B. Weiss, and J. J. Weis Gene Expression Profiling Reveals Unique Pathways Associated with Differential Severity of Lyme Arthritis J. Immunol., December 1, 2006; 177(11): 7930 - 7942. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Kaplan and M. Linial ProtoBee: Hierarchical classification and annotation of the honey bee proteome Genome Res., November 1, 2006; 16(11): 1431 - 1438. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Richard, R. Roepman, W. M. Aartsen, A. G.S.H. van Rossum, A. I. den Hollander, E. Knust, J. Wijnholds, and F. P.M. Cremers Towards understanding CRUMBS function in retinal dystrophies Hum. Mol. Genet., October 15, 2006; 15(suppl_2): R235 - R243. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Zhang, C. J. Martyniuk, and V. L. Trudeau SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation Bioinformatics, October 15, 2006; 22(20): 2459 - 2462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Soderlund, W. Nelson, A. Shoemaker, and A. Paterson SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res., September 1, 2006; 16(9): 1159 - 1168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Eddy and N. Maizels Gene function correlates with potential for G4 DNA formation in the human genome Nucleic Acids Res., September 1, 2006; 34(14): 3887 - 3896. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. J. Rigby, M. M. A. Fernando, and T. J. Vyse Mice, humans and haplotypes--the hunt for disease genes in SLE Rheumatology, September 1, 2006; 45(9): 1062 - 1067. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. F. Fiol, S. Y. Chan, and D. Kultz Regulation of osmotic stress transcription factor 1 (Ostf1) in tilapia (Oreochromis mossambicus) gill epithelium during salinity stress J. Exp. Biol., August 15, 2006; 209(16): 3257 - 3265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Greenman, R. Wooster, P. A. Futreal, M. R. Stratton, and D. F. Easton Statistical Analysis of Pathogenicity of Somatic Mutations in Cancer Genetics, August 1, 2006; 173(4): 2187 - 2198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kim, K. Melen, M. Osterberg, and G. von Heijne A global topology map of the Saccharomyces cerevisiae membrane proteome PNAS, July 25, 2006; 103(30): 11142 - 11147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Berg and M. Lassig Cross-species analysis of biological networks by Bayesian alignment PNAS, July 18, 2006; 103(29): 10967 - 10972. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Al-Shahrour, P. Minguez, J. Tarraga, D. Montaner, E. Alloza, J. M. Vaquerizas, L. Conde, C. Blaschke, J. Vera, and J. Dopazo BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W472 - W476. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Conde, J. M. Vaquerizas, H. Dopazo, L. Arbiza, J. Reumers, F. Rousseau, J. Schymkowitz, and J. Dopazo PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W621 - W625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Han, H. J. Kang, Y. Cho, S. Lee, Y. J. Kim, and S. Gong SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W642 - W644. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Schenten, A. Egert, M. Pasparakis, and K. Rajewsky M17, a gene specific for germinal center (GC) B cells and a prognostic marker for GC B-cell lymphomas, is dispensable for the GC reaction in mice Blood, June 15, 2006; 107(12): 4849 - 4856. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Ek, U. Andreasson, S. Hober, C. Kampf, F. Ponten, M. Uhlen, H. Merz, and C. A. K. Borrebaeck From Gene Expression Analysis to Tissue Microarrays: A Rational Approach to Identify Therapeutic and Diagnostic Targets in Lymphoid Malignancies Mol. Cell. Proteomics, June 1, 2006; 5(6): 1072 - 1081. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Grassot, M. Gouy, G. Perriere, and G. Mouchiroud Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-Like Domains Mol. Biol. Evol., June 1, 2006; 23(6): 1232 - 1241. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. van Baren and M. R. Brent Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res., May 1, 2006; 16(5): 678 - 685. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Nolan, L. Wu, H. J. Bang, S. A. Jelinsky, K. P. Roberts, T. T. Turner, G. S. Kopf, and D. S. Johnston Identification of Rat Cysteine-Rich Secretory Protein 4 (Crisp4) as the Ortholog to Human CRISP1 and Mouse Crisp4 Biol Reprod, May 1, 2006; 74(5): 984 - 991. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ezawa, S. OOta, and N. Saitou Genome-Wide Search of Gene Conversions in Duplicated Genes of Mouse and Rat Mol. Biol. Evol., May 1, 2006; 23(5): 927 - 940. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. K. McEwen, A. Woolfe, D. Goode, T. Vavouri, H. Callaway, and G. Elgar Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Genome Res., April 1, 2006; 16(4): 451 - 465. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Pellegrini-Calace and A. Tramontano Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches Bioinformatics, April 1, 2006; 22(7): 775 - 778. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang and X. Wang Systematic identification of microRNA functions by combining target prediction and expression profiling Nucleic Acids Res., March 20, 2006; 34(5): 1646 - 1652. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. B. Montgomery, O. L. Griffith, M. C. Sleumer, C. M. Bergman, M. Bilenky, E. D. Pleasance, Y. Prychyna, X. Zhang, and S. J. M. Jones ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation Bioinformatics, March 1, 2006; 22(5): 637 - 640. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Semon, J. R. Lobry, and L. Duret No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans Mol. Biol. Evol., March 1, 2006; 23(3): 523 - 529. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Castrignano, P. D. De Meo, G. Grillo, S. Liuni, F. Mignone, I. G. Talamo, and G. Pesole GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags Bioinformatics, February 15, 2006; 22(4): 497 - 499. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Sauer, E. Shelest, and E. Wingender Evaluating phylogenetic footprinting for human-rodent comparisons Bioinformatics, February 15, 2006; 22(4): 430 - 437. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Rothganger, M. Weniger, T. Weniger, A. Mellmann, and D. Harmsen Ridom TraceEdit: a DNA trace editor and viewer Bioinformatics, February 15, 2006; 22(4): 493 - 494. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ecroyd, M. Belghazi, J.-L. Dacheux, M. Miyazaki, T. Yamashita, and J.-L. Gatti An Epididymal Form of Cauxin, a Carboxylesterase-Like Enzyme, Is Present and Active in Mammalian Male Reproductive Fluids Biol Reprod, February 1, 2006; 74(2): 439 - 447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Menendez, O. Krysiak, A. Inga, B. Krysiak, M. A. Resnick, and G. Schonfelder A SNP in the flt-1 promoter integrates the VEGF system into the p53 transcriptional network PNAS, January 31, 2006; 103(5): 1406 - 1411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Stamm, J.-J. Riethoven, V. Le Texier, C. Gopalakrishnan, V. Kumanduri, Y. Tang, N. L. Barbosa-Morais, and T. A. Thanaraj ASD: a bioinformatics resource on alternative splicing Nucleic Acids Res., January 1, 2006; 34(suppl_1): D46 - D55. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Robertson, M. Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O. L. Griffith, X. Zhang, et al. cisRED: a database system for genome-scale computational discovery of regulatory elements Nucleic Acids Res., January 1, 2006; 34(suppl_1): D68 - D73. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|