The Vertebrate Genome Annotation (Vega) database

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Ashurst, J L ^a   Chen, C K ^a   Gilbert, J G R ^a   Jekosch, K ^a   Keenan, S ^a   Meidl, P ^a   Searle, S M ^a   Stalker, J ^a   Storey, R ^a   Trevanion, S ^a   Wilming, L ^a   Hubbard, T ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; COMPARATIVE STUDY; GENE SEQUENCE; GENE STRUCTURE; GENETIC DATABASE; GENETIC DIFFERENCE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; HUMAN CHROMOSOME; IMAGE DISPLAY; INFORMATION PROCESSING; MOUSE; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PUBLISHING; QUALITY CONTROL; STANDARDIZATION; VERTEBRATE; VERTEBRATE GENOME ANNOTATION; ZEBRA FISH; CHROMOSOME; COMPUTER PROGRAM; GENOME; INTERNET; VERTEBRATE GENOME ANNOTATION DATABASE;

ANIMALS; CHROMOSOMES, HUMAN; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENOME; GENOMICS; HUMANS; MICE; USER-COMPUTER INTERFACE; VERTEBRATES; ZEBRAFISH;

DANIO RERIO; VERTEBRATA;

EID: 13444304332     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki135     Document Type: Article

References (29)

1. Dunham,I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R., Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J. et al. (1999) The DNA sequence of human chromosome 22. Nature, 402 489-495.
2. Birney,E., Andrews,T.D., Bevan,P., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cuff,J., Curwen,V., Cutts,T. et al. (2004) An overview of Ensembl. Genome Res., 14, 925-928.
3. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
4. Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C., Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409 860-921.
5. Mallon,A.-M., Wilming,L., Weekes,J., Gilbert,J.G.R., Ashurst,J., Peyrefitte,S., Matthews,L., Cadman,M., McKeone,R., Sellick,C.A. et al. (2004) 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., 14, 1888-1901.
6. Deloukas,P., Matthews,L.H., Ashurst,J., Burton,J., Gilbert,J.G., Jones,M., Stavrides,G., Almeida,J.P., Babbage,A.K., Bagguley,C.L. et al. (2001) The DNA sequence and comparative analysis of human chromosome 20. Nature, 414, 865-871.
7. Heilig,R., Eckenberg,R., Petit,J.L., Fonknechten,N., Da Silva,C., Cattolico,L., Levy,M., Barbe,V., De Berardinis,V., Ureta-Vidal,A. et al. (2003) The DNA sequence and analysis of human chromosome 14. Nature, 421, 601-607
8. Ashurst,J.L. and Collins,J.E. (2003) Gene annotation: prediction and testing. Annu. Rev. Genomics Hum. Genet., 4, 69-88.
9. Blake,J.A., Richardson,J.E., Bult,C.J., Kadin,J.A. and Eppig,J.T. (2003) MGD: the Mouse Genome Database. Nucleic Acids Res. 31, 193-195.
10. Sprague,J., Clements,D., Conlin,T., Edwards,P., Frazer,K., Schaper,K., Segerdell,E., Song,P., Sprunger,B. and Westerfield,M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res., 31, 241-243.
11. Wheeler,D.L., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E. et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res., 32 D35-D40.
12. Wain,H.M., Lush,M.J., Ducluzeau,F., Khodiyar,V.K. and Povey,S. (2004) Genew: the Human Gene Nomenclature Database, 2004 updates. Nucleic Acids Res., 32, D255-D257.
13. Searle,S.M., Gilbert,J., Iyer,V. and Clamp,M. (2004) The otter annotation system. Genome Res., 14, 963-970.
14. Winter,J., Lehmann,T., Krauss,S., Trockenbacher,A., Kijas,Z., Foerster,J., Suckow,V., Yaspo,M.L., Kulozik,A., Kalscheuer,V. et al. (2004) Regulation of the MID1 protein function is fine-tuned by a complex pattern of alternative splicing. Hum. Genet., 114, 541-552.
15. Stewart,C.A., Horton,R., Allcock,R.J., Ashurst,J.L., Atrazhev,A.M., Coggill,P., Dunham,I., Forbes,S., Halls,K., Howson,J.M. et al. (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res., 14, 1176-1187.
16. Hill,N.J., Lyons,P.A., Armitage,N., Todd,J.A., Wicker,L.S. and Peterson,L.B. (2000) NOD Idd5 locus controls insulitis and diabetes and overlaps the orthologous CTLA4/IDDM12 and NRAMP1 loci in humans. Diabetes, 49, 1744-1747.
17. Wicker,L.S., Chamberlain,G., Hunter,K., Rainbow,D., Howlett,S., Tiffen,P., Clark,J., Gonzalez-Munoz,A., Cumiskey,A.M., Rosa,R.L. et al. (2004) Fine mapping, gene content, comparative sequencing, and expression analyses support Ctla4 and Nramp1 as candidates for Idd5.1 and Idd5.2 in the nonobese diabetic mouse. J. Immunol., 173, 164-173.
18. Kasprzyk,A., Keefe,D., Smedley,D., London,D., Spooner,W., Melsopp,C., Hammond,M., Rocca-Serra,P., Cox,T. and Birney,E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
19. The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
20. Potter,S.C., Clarke,L., Curwen,V., Keenan,S., Mongin,E., Searle,S.M.J., Stabenau,A., Storey,R. and Clamp,M. (2004) The Ensembl Analysis Pipeline. Genome Res., 14, 934-941.
21. Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
22. Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
23. Mott,R. (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl., 13, 477-478.
24. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L.L. et al. (2004) The Pfam Protein Families Database. Nucleic Acids Res., 32, D138-D141.
25. Birney,E., Clamp,M. and Durbin,R. (2004) GeneWise and Genomewise. Genome Res., 14, 988-995.
26. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
27. Salamov,A.A. and Solovyev,V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10, 516-522.
28. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
29. Down,T.A. and Hubbard,T.J.P. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res., 12, 458-461.