Development and public release of a comprehensive hepatitis virus database
Development and public release of a comprehensive hepatitis virus database
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DOI：
10.1111/j.1872-034x.2007.00262.x
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发表时间：
2008-03-01
影响因子：
4.2
通讯作者：
Mizokami, Masashi
中科院分区：
文献类型：
--
作者：
Shin-I, Tadasu;Tanaka, Yasuhito;Mizokami, Masashi
目的：目前，国际核苷酸序列数据库协作组织（INSDC，以前称为DDBJ/EMBL/GenBank）中提供了大约44 000个丙型肝炎病毒（HCV）、11 000个乙型肝炎病毒（HBV）和1600个戊型肝炎病毒（HEV）序列，并且这些病毒序列的数量正在快速增长。然而，由于 INDSC 并不专门针对肝炎病毒，因此很难从中检索病毒学或临床兴趣的信息。因此，构建一个专门的肝炎病毒序列数据库并使其可供全世界研究人员使用是非常值得的。方法：我们开发了一个基于WWW的数据库肝炎病毒数据库（HVDB），其中包含INSDC可用的所有HCV、HBV和HEV序列。在HVDB中，从INSDC获得的所有片段序列都被排列到每种病毒的基因组序列中。数据库中还给出了每种病毒变体之间基因组上每个位点的系统发育关系。结果：数据库用户可以通过参考系统发育关系轻松检索特定基因型的条目（带注释的序列）或通过参考基因组图谱信息检索特定位点的系统发育关系。 HVDB为用户提供了一个系统发育分析工具，可以与数据检索工具结合使用。结论：最新版本可在HVDB网站上公开访问：http://s2as02.genes.nig.ac.jp。
Aim: Currently, approximately 44 000 hepatitis C virus (HCV), 11 000 hepatitis B virus (HBV), and 1600 hepatitis E virus (HEV) sequences are available at the International Nucleotide Sequence Database Collaboration (INSDC, previously known as DDBJ/EMBL/GenBank), and the number of these virus sequences is growing rapidly. However, since INDSC is not specialized to hepatitis viruses, it is difficult to retrieve information of virological or clinical interests from it. Thus, it is quite worthwhile to construct a specialized database for the hepatitis virus sequences and to make it accessible to researchers worldwide.Methods: We developed a WWW-based database hepatitis virus database (HVDB), which contains all the HCV, HBV, and HEV sequences available at INSDC. In the HVDB, all piece sequences obtained from INSDC are arranged to the genomesequence of each virus. Also given in the database are the phylogenetic relationships of each locus on the genome among variants for each virus.Results: Users of the database can easily retrieve entries (sequences with annotations) of the specific genotype by referring to the phylogenetic relationships or those of specific loci by referring to the genome map information. HVDB provides users with a tool for phylogenetic analysis that can be used in combination with the data retrieval tools.Conclusion: The latest release is publicly accessible at the HVDB website: http://s2as02.genes.nig.ac.jp.