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The vertebrate genome annotation (Vega) database

L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard, J. L. Harrow
2007 Nucleic Acids Research  
annotation groups for providing the annotation data that currently incorporated into Vega.  ...  We thank the Ensembl Project for the software that is the basis of the Vega website and the Otter client/server.  ...  The Vega database is the central repository for the majority of genome sequencing centres to deposit their annotation of human chromosomes.  ... 
doi:10.1093/nar/gkm987 pmid:18003653 pmcid:PMC2238886 fatcat:hhqymtfqxzdp5keyrz6mizlve4

The Vertebrate Genome Annotation (Vega) database

J. L. Ashurst
2004 Nucleic Acids Research  
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  ...  In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences.  ...  ACKNOWLEDGEMENTS We thank the Havana, Chromosome 22, Genoscope and WashU genome annotation groups for providing the annotation data that have been currently incorporated into Vega.  ... 
doi:10.1093/nar/gki135 pmid:15608237 pmcid:PMC540089 fatcat:isoio6kzqvh3tilxim6eqczvqu

The importance of identifying alternative splicing in vertebrate genome annotation

Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer Harrow
2012 Database: The Journal of Biological Databases and Curation  
We describe our detailed manual annotation of vertebrate genomes, which is generating a publicly available geneset rich in AS.  ...  While alternative splicing (AS) can potentially expand the functional repertoire of vertebrate genomes, relatively few AS transcripts have been experimentally characterized.  ...  AS is observed at a high frequency in vertebrates (3), but has also been shown to occur in invertebrate, plant and fungal genomes (4) (5) (6) (7) .  ... 
doi:10.1093/database/bas014 pmid:22434846 pmcid:PMC3308168 fatcat:26zcrc2mijfvvbmk5ar3l4nqre

The Vertebrate Genome Annotation browser 10 years on

Jennifer L. Harrow, Charles A. Steward, Adam Frankish, James G. Gilbert, Jose M. Gonzalez, Jane E. Loveland, Jonathan Mudge, Dan Sheppard, Mark Thomas, Stephen Trevanion, Laurens G. Wilming
2013 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank the HAVANA team for providing annotation of the reference genomes, and also the immune response annotation group (IRAG) that provided community annotation for the pig immunome  ...  We also thank our nomenclature collaborators (HGNC, ZFIN, MGI and RGD) that provide official nomenclature for VEGA genes.  ...  INTRODUCTION In 2014, the Vertebrate Genome Annotation (VEGA) (http://vega.sanger.ac.uk) browser will celebrate its 10th anniversary.  ... 
doi:10.1093/nar/gkt1241 pmid:24316575 pmcid:PMC3964964 fatcat:2ut4jvn3kffxzkqnd3ppj7sd2a

Community gene annotation in practice

J. E. Loveland, J. G. R. Gilbert, E. Griffiths, J. L. Harrow
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank Professor Christopher Tuggle and Dr Claire Rogel-Gaillard, the members of the KOMP, NorCOMM and IRAG annotation groups and the Havana annotation team.  ...  The manual annotation from the Havana team is released every three months and publicly available from the Vertebrate Genome Annotation Database (VEGA) database (3).  ...  The Otterlace database schema is based on the Ensembl schema. The annotation data is stored in a MySQL database (19) and forms the backend to the Vega database.  ... 
doi:10.1093/database/bas009 pmid:22434843 pmcid:PMC3308165 fatcat:lbqygrvrwjgsjkxjov6eafakbe

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong, Robert D. Finn
2016 Database: The Journal of Biological Databases and Curation  
However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used  ...  Abstract The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation.  ...  , profiles or patterns). 10.0, the latest PANTHER version at the time of writing, included 22 new genomes in their phylogenetic trees, expanding from 82 to 104 genomes; 250 families were merged into other  ... 
doi:10.1093/database/baw027 pmid:26994912 pmcid:PMC4799721 fatcat:lwve4cepezbcvi6t2k6odynq4u

Las Vegas algorithms for gene recognition

Sing-Hoi Sze, Pavel A. Pevzner
1997 Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97  
Use of these predictions for sequence annotation in databases is hardly possible since it would create a clutter of unreliable feature tables.  ...  For each genomic sequence, a list of relat,cd proteins was construct,ed using the ENTREZ database of BLAST similarity scores.  ... 
doi:10.1145/267521.267889 dblp:conf/recomb/SzeP97 fatcat:6jr33ds2wnhixagxanfhn7zkx4

Mouse genome database 2016

Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson
2015 Nucleic Acids Research  
The Mouse Genome Database (MGD; http://www. informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related  ...  Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of  ...  The Mouse Genome Database (MGD) is the primary community resource for integrated genetic, genomic, functional and phenotypic information supporting the link between mouse models and human phenotypes and  ... 
doi:10.1093/nar/gkv1211 pmid:26578600 pmcid:PMC4702860 fatcat:ufv3jxfe55fdljxozjt6gzuayi

The Zebrafish Information Network: the zebrafish model organism database

J. Sprague
2006 Nucleic Acids Research  
Recent enhancements to ZFIN include (i) comprehensive curation of gene expression data from the literature and from directly sub-20 mitted data, (ii) increased support and annotation of the genome sequence  ...  10 The Zebrafish Information Network (ZFIN; http://zfin. org) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data.  ...  ACKNOWLEDGEMENTS 5 Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkj086 pmid:16381936 pmcid:PMC1347449 fatcat:hn2czv6dkbg2rjpedqetwwym5i

The Mouse Genome Database: enhancements and updates

Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T Eppig
2009 Nucleic Acids Research  
The Mouse Genome Database (MGD) is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) database resource and serves as the primary community model organism database  ...  MGD is the authoritative source for mouse gene, allele and strain nomenclature and for phenotype and functional annotations of mouse genes.  ...  .ucsc.edu) and the Vertebrate Genome Annotation (Vega) group (http://vega.sanger.ac.uk/index.html), to maintain a comprehensive catalog of mouse genes and other genome features, and also to resolve inconsistencies  ... 
doi:10.1093/nar/gkp880 pmid:19864252 pmcid:PMC2808942 fatcat:4azrklowubgqxfc7fogb5644ei

The UCSC Genome Browser Database: update 2006

A. S. Hinrichs
2006 Nucleic Acids Research  
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms.  ...  The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome.  ...  ACKNOWLEDGEMENTS The UCSC GBD project is funded by grants from the National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI) and the National Cancer Institute (NCI).  ... 
doi:10.1093/nar/gkj144 pmid:16381938 pmcid:PMC1347506 fatcat:fdhl3rwlpnclnox2lrd3k7e7se

The UCSC genome browser database: update 2007

R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead (+13 others)
2007 Nucleic Acids Research  
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms.  ...  The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome.  ...  ACKNOWLEDGEMENTS The UCSC GBD project is funded by grants from the National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI) and the National Cancer Institute (NCI).  ... 
doi:10.1093/nar/gkl928 pmid:17142222 pmcid:PMC1669757 fatcat:5h65fma2trhvpcjy4glloar4ha

Sequencing and comparative analysis of the gorilla MHC genomic sequence

Laurens G. Wilming, Elizabeth A. Hart, Penny C. Coggill, Roger Horton, James G. R. Gilbert, Chris Clee, Matt Jones, Christine Lloyd, Sophie Palmer, Sarah Sims, Siobhan Whitehead, David Wiley (+2 others)
2013 Database: The Journal of Biological Databases and Curation  
Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome.  ...  Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.  ...  Acknowledgements The author would like to thank the members of the sequencing, sequence finishing and HAVANA teams for their invaluable contribution.  ... 
doi:10.1093/database/bat011 pmid:23589541 pmcid:PMC3626023 fatcat:2bmtlzpn35cdpfozqxnvcd6ozy

The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes

Charles A. Steward, Jose M. Gonzalez, Steve Trevanion, Dan Sheppard, Giselle Kerry, James G. R. Gilbert, Linda S. Wicker, Jane Rogers, Jennifer L. Harrow
2013 Database: The Journal of Biological Databases and Curation  
Furthermore, we have established that the variation rate in the Idd regions is 2.3 times higher than the mean found for the whole genome assembly for the NOD/ShiLtJ genome, which we suggest reflects the  ...  The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes.  ...  Acknowledgements The authors thank Thomas Keane for his advice and help with the variation calling and the teams in mapping, sequence production, finishing, annotation and analysis for their contributions  ... 
doi:10.1093/database/bat032 pmid:23729657 pmcid:PMC3668384 fatcat:erziwmzbzbhyld255qmq5xgvkm

SHIELD: an integrative gene expression database for inner ear research

Jun Shen, Déborah I. Scheffer, Kelvin Y. Kwan, David P. Corey
2015 Database: The Journal of Biological Databases and Curation  
These datasets are combined in a relational database that integrates experimental data and annotations relevant to the inner ear.  ...  Database (SHIELD), an integrated resource that seeks to compile, organize and analyse the genomic, transcriptomic and proteomic knowledge of the inner ear.  ...  Acknowledgements The authors thank Dr Peter Barr-Gillespie, Dr Zheng-Yi Chen, Dr Lisa Goodrich and Dr David Z.Z.  ... 
doi:10.1093/database/bav071 pmid:26209310 pmcid:PMC4513695 fatcat:rk22su65avcytkw4emuitj52j4
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