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      Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes

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          Abstract

          Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

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          Nucleotide sequence of bacteriophage phi X174 DNA.

          F. Sanger, G Air, B G Barrell … (1977)
          A DNA sequence for the genome of bacteriophage phi X174 of approximately 5,375 nucleotides has been determined using the rapid and simple 'plus and minus' method. The sequence identifies many of the features responsible for the production of the proteins of the nine known genes of the organism, including initiation and termination sites for the proteins and RNAs. Two pairs of genes are coded by the same region of DNA using different reading frames.
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            DPVweb: a comprehensive database of plant and fungal virus genes and genomes

            Michael Adams, John Antoniw (2005)
            DPVweb () provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n ≈ 9000). For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses.
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              Characterization of a highly pathogenic H5N1 influenza virus derived from bar-headed geese in China.

              Gang Shen, Xin Liu, Chun-Yang Zhen … (2006)
              Influenza A viruses are usually non-pathogenic in wild aquatic birds, their natural reservoir. However, from May to July 2005, at Qinghai Lake in China, an unprecedented outbreak of highly pathogenic H5N1 avian influenza virus caused the death of thousands of wild migratory waterbirds. Herein, H5N1 influenza virus from bar-headed geese collected during the outbreak was characterized. Genomic analysis showed that A/Bar-headed Goose/Qinghai/0510/05 (Bh H5N1 virus) is a reassortant virus. Amino acid residue (lysine) at position 627 in the PB2 gene of the Bh H5N1 virus was the same as that of the human H5N1 virus (A/HK/483/97) and different from that of H5N1 avian influenza viruses deposited in GenBank. Antigenic analysis showed that significant antigenic variation has occurred in the Bh H5N1 virus. The Bh H5N1 virus induced systemic infections and caused 100 % mortality in chickens and mice, and 80 % mortality in ducks and geese. Bh H5N1 virus titres were higher in multiple organs of chickens, ducks and geese than in mice, and caused more severe histological lesions in chickens, ducks and mice than in geese. These results support the need to pay close attention and create control programmes to prevent the transmission of highly pathogenic avian influenza virus from wild migratory waterbirds into domestic chickens, ducks, geese and mammalian hosts.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (pmc): nar
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2007
                Publication date (Electronic): 7 December 2006
                Publication date PMC-release: 07 December 2006
                Volume: 35
                Issue: Database issue
                Pages: D339-D342
                Affiliations
                Center for Information Biology and DNA Data Bank of Japan National Institute of Genetics and Sokendai Shizuoka, Japan
                1Faculty of Pharmaceutical Sciences, Tokyo University of Science Chiba, Japan
                2Life Science Systems Division, Fujitsu Limited Tokyo, Japan
                Author notes
                *To whom correspondence should be addressed. Tel: +81 55 981 6895; Fax: +81 55 981 6896; Email: hsugawar@ 123456genes.nig.ac.jp
                Article
                DOI: 10.1093/nar/gkl1004
                PMC ID: 1781101
                PubMed ID: 17158166
                SO-VID: d6edeb58-15b8-4c7d-b9e3-5097967c5ade
                Copyright statement: © 2006 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 15 September 2006
                Date revision received : 27 October 2006
                Date accepted : 27 October 2006
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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