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PMID: 15608237 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The Vertebrate Genome Annotation (Vega) database.

Nucleic acids research ·Vol. 33 ·No. Database issue ·2005-01-01 ·Pages D459-65

Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S, Wilming L, Hubbard T

Abstract

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.

MeSH Terms

Animals Chromosomes, Human/chemistry Database Management Systems Databases, Genetic/standards Genome Genomics Humans Mice User-Computer Interface Vertebrates/genetics Zebrafish/genetics

Authors & Affiliations

12 authors, click to expand affiliations / ORCID

Ashurst J L

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. [email protected]

Chen C-K

Gilbert J G R

Jekosch K

Keenan S

Meidl P

Searle S M

Stalker J

Storey R

Trevanion S

Wilming L

Hubbard T

References (29)

29 references, click to expand

The DNA sequence of human chromosome 22.
Nature. 1999 Dec 2;402(6761):489-95 PMID: 10591208
Tandem repeats finder: a program to analyze DNA sequences.
Nucleic Acids Res. 1999 Jan 15;27(2):573-80 PMID: 9862982
EMBOSS: the European Molecular Biology Open Software Suite.
Trends Genet. 2000 Jun;16(6):276-7 PMID: 10827456
NOD Idd5 locus controls insulitis and diabetes and overlaps the orthologous CTLA4/IDDM12 and NRAMP1 loci in humans.
Diabetes. 2000 Oct;49(10):1744-7 PMID: 11016460
Initial sequencing and analysis of the human genome.
Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
The DNA sequence and comparative analysis of human chromosome 20.
Nature. 2001 Dec 20-27;414(6866):865-71 PMID: 11780052
Computational detection and location of transcription start sites in mammalian genomic DNA.
Genome Res. 2002 Mar;12(3):458-61 PMID: 11875034
The human genome browser at UCSC.
Genome Res. 2002 Jun;12(6):996-1006 PMID: 12045153
MGD: the Mouse Genome Database.
Nucleic Acids Res. 2003 Jan 1;31(1):193-5 PMID: 12519980
The Zebrafish Information Network (ZFIN): the zebrafish model organism database.
Nucleic Acids Res. 2003 Jan 1;31(1):241-3 PMID: 12519991
The DNA sequence and analysis of human chromosome 14.
Nature. 2003 Feb 6;421(6923):601-7 PMID: 12508121
Gene annotation: prediction and testing.
Annu Rev Genomics Hum Genet. 2003;4:69-88 PMID: 14527297
Database resources of the National Center for Biotechnology Information: update.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D35-40 PMID: 14681353
The Pfam protein families database.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41 PMID: 14681378
Genew: the Human Gene Nomenclature Database, 2004 updates.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D255-7 PMID: 14681406
EnsMart: a generic system for fast and flexible access to biological data.
Genome Res. 2004 Jan;14(1):160-9 PMID: 14707178
Regulation of the MID1 protein function is fine-tuned by a complex pattern of alternative splicing.
Hum Genet. 2004 May;114(6):541-52 PMID: 15057556
An overview of Ensembl.
Genome Res. 2004 May;14(5):925-8 PMID: 15078858
The Ensembl analysis pipeline.
Genome Res. 2004 May;14(5):934-41 PMID: 15123589
The otter annotation system.
Genome Res. 2004 May;14(5):963-70 PMID: 15123593
GeneWise and Genomewise.
Genome Res. 2004 May;14(5):988-95 PMID: 15123596
Complete MHC haplotype sequencing for common disease gene mapping.
Genome Res. 2004 Jun;14(6):1176-87 PMID: 15140828
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. 2004 Jul 1;173(1):164-73 PMID: 15210771
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. 2004 Oct;14(10A):1888-901 PMID: 15364904
The ENCODE (ENCyclopedia Of DNA Elements) Project.
Science. 2004 Oct 22;306(5696):636-40 PMID: 15499007
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Res. 1997 Mar 1;25(5):955-64 PMID: 9023104
Prediction of complete gene structures in human genomic DNA.
J Mol Biol. 1997 Apr 25;268(1):78-94 PMID: 9149143
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA.
Comput Appl Biosci. 1997 Aug;13(4):477-8 PMID: 9283765
Ab initio gene finding in Drosophila genomic DNA.
Genome Res. 2000 Apr;10(4):516-22 PMID: 10779491

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gki135

[email protected]

Published

2005-01-01

Pages

D459-65

Language

English

Region

England

NLM ID

0411011

PMCID

PMC540089

Subset

External Links

PubMed source DOI: 10.1093/nar/gki135 PMC Full Text View journal details

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