The vertebrate genome annotation (Vega) database

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

[1]  Sophie Palmer,et al.  Complete MHC haplotype sequencing for common disease gene mapping. , 2004, Genome research.

[2]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[3]  Monte Westerfield,et al.  The Zebrafish Information Network: the zebrafish model organism database , 2005, Nucleic Acids Res..

[4]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[5]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[6]  Melanie E. Goward,et al.  The DNA sequence of human chromosome 22 , 1999, Nature.

[7]  D. Coleman,et al.  Three recessive loci required for insulin-dependent diabetes in nonobese diabetic mice. , 1987, Science.

[8]  Don Gilbert,et al.  Software review: Shopping in the genome market with EnsMart , 2003, Briefings Bioinform..

[9]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[10]  Judith A. Blake,et al.  MGD: the Mouse Genome Database , 2003, Nucleic Acids Res..

[11]  Monte Westerfield,et al.  The Zebrafish Information Network (ZFIN): the zebrafish model organism database , 2003, Nucleic Acids Res..

[12]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[13]  Andreas Kulozik,et al.  Regulation of the MID1 protein function is fine-tuned by a complex pattern of alternative splicing , 2004, Human Genetics.

[14]  Areum Han,et al.  SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay , 2007, Bioinform..

[15]  J. Todd,et al.  NOD Idd5 locus controls insulitis and diabetes and overlaps the orthologous CTLA4/IDDM12 and NRAMP1 loci in humans. , 2000, Diabetes.

[16]  S Forbes,et al.  The MHC haplotype project: a resource for HLA-linked association studies. , 2002, Tissue antigens.

[17]  Jan-Fang Cheng,et al.  Primate-specific evolution of an LDLR enhancer , 2006, Genome Biology.

[18]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database , 2002, Nucleic Acids Res..

[19]  S. Searle,et al.  The Ensembl analysis pipeline. , 2004, Genome research.

[20]  J. Todd,et al.  Genetic control of autoimmune diabetes in the NOD mouse. , 1995, Annual review of immunology.

[21]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[22]  Richard Mott,et al.  EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA , 1997, Comput. Appl. Biosci..

[23]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database, 2004 updates , 2004, Nucleic Acids Res..

[24]  J. Ashurst,et al.  Gene annotation: prediction and testing. , 2003, Annual review of genomics and human genetics.

[25]  Paul A Lyons,et al.  Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. , 2002, Genome research.

[26]  D R Bentley,et al.  The DNA sequence and comparative analysis of human chromosome 20 , 2004, Nature.

[27]  Hagen Blankenburg,et al.  The implications of alternative splicing in the ENCODE protein complement , 2007, Proceedings of the National Academy of Sciences.

[28]  Patrick Wincker,et al.  The DNA sequence and analysis of human chromosome 14 , 2023, Nature.

[29]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[30]  Jane Rogers,et al.  Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17 , 2007, Genome Biology.

[31]  S Beck,et al.  The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studies. , 2006, Tissue antigens.

[32]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[33]  Sophie Palmer,et al.  Genetic Analysis of Completely Sequenced Disease-Associated MHC Haplotypes Identifies Shuffling of Segments in Recent Human History , 2006, PLoS genetics.

[34]  Simon C. Potter,et al.  An overview of Ensembl. , 2004, Genome research.

[35]  James G. R. Gilbert,et al.  The Vertebrate Genome Annotation (Vega) database , 2004, Nucleic acids research.

[36]  Vivek Iyer,et al.  The otter annotation system. , 2004, Genome research.

[37]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[38]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[39]  E. Birney,et al.  EGASP: the human ENCODE Genome Annotation Assessment Project , 2006, Genome Biology.

[40]  T. Hubbard,et al.  Computational detection and location of transcription start sites in mammalian genomic DNA. , 2002, Genome research.

[41]  J. Harrow,et al.  GENCODE: producing a reference annotation for ENCODE , 2006, Genome Biology.

[42]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[43]  Luc J. Smink,et al.  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 1 , 2004, The Journal of Immunology.

[44]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[45]  D. Gilbert.  Shopping in the genome market with EnsMart. , 2003, Briefings in bioinformatics.

[46]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[47]  S Beck,et al.  The genomic sequence and analysis of the swine major histocompatibility complex. , 2006, Genomics.

[48]  I. Dunham,et al.  DNA sequence and analysis of human chromosome 9 , 2003, Nature.

[49]  Linda S. Wicker,et al.  NOD Idd 5 Locus Controls Insulitis and Diabetes and Overlaps the Orthologous CTLA 4 / IDDM 12 and NRAMP 1 Loci in Humans , 2000 .

[50]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[51]  The BioSapiens Network of Excellence.  Research Networks: BioSapiens: a European network for integrated genome annotation , 2005, European Journal of Human Genetics.

[52]  John M. Hancock,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. , 2004, Genome research.

[53]  Sophie Palmer,et al.  Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6q , 2006, Immunogenetics.

[54]  Michael A Quail,et al.  Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species. , 2005, Genomics.