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      ViralZone: recent updates to the virus knowledge resource

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          Abstract

          ViralZone ( http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host–virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

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          Most cited references19

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          The Universal Protein Resource (UniProt) in 2010

          The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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            NCBI Reference Sequences: current status, policy and new initiatives

            NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system.
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              ViralZone: a knowledge resource to understand virus diversity

              The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2013
                January 2013
                27 November 2012
                27 November 2012
                : 41
                : D1 , Database issue
                : D579-D583
                Affiliations
                1SIB Swiss Institute of Bioinformatics, Swiss-Prot Group, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland, 2Translational Research Sciences, Hoffmann-La Roche Drug Discovery & Early Development, 340 Kingsland Street, Nutley, NJ 07110NJ, USA, 3Hoffmann La Roche, Bioinformatics and Exploratory Statistics Department, pRED, Grenzacherstrasse 124, 4070 Basel, Switzerland and 4SIB Swiss Institute of Bioinformatics, Vital-IT Group, Quartier Sorge—Bâtiment Génopode, 1015, Lausanne, Switzerland
                Author notes
                *To whom correspondence should be addressed. Tel: +41 22 379 58 70; Fax: +41 22 379 58 58; Email: philippe.lemercier@ 123456isb-sib.ch
                Article
                gks1220
                10.1093/nar/gks1220
                3531065
                23193299
                d9596297-1cab-4f9d-924d-980783c8ef8b
                © The Author(s) 2012. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

                History
                : 15 September 2012
                : 26 October 2012
                : 31 October 2012
                Page count
                Pages: 5
                Categories
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                Genetics
                Genetics

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