HOVERGEN - A DATABASE OF HOMOLOGOUS VERTEBRATE GENES
HOVERGEN - A DATABASE OF HOMOLOGOUS VERTEBRATE GENES
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DOI：
10.1093/nar/22.12.2360
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发表时间：
1994-06-25
影响因子：
14.9
通讯作者：
GOUY, M
中科院分区：
文献类型：
--
作者：
DURET, L;MOUCHIROUD, D;GOUY, M
同源基因的比较是许多与基因组结构、功能或进化有关的研究的重要步骤。相似性搜索程序很容易找到与给定序列同源的基因。然而，只有非常繁琐的人工程序允许检索所有的同源基因序列为一组给定的物种。此外，由于同时管理的数据的复杂性，这种搜索经常产生错误：系统发育树、比对、分类、序列和相关信息。HOVERGEN通过整合所有这些信息来帮助解决这些问题。HOVERGEN对应于所有脊椎动物物种的GenBank序列，其中一些数据经过纠正，澄清或完成，特别是解决冗余问题。编码序列在基因家族中被分类。计算了每个家族的蛋白质多重比对和系统发育树。序列和相关信息已在ACNUC数据库中结构化，允许进行复杂的选择。已经开发了一个图形界面来可视化和编辑树。根据它们的分类，基因以颜色显示。用户只需点击基因，就可以直接访问附加到序列和多个比对的所有信息。因此，这个图形工具提供了一个快速和简单的访问所有必要的数据来解释基因之间的同源关系。HOVERGEN允许用户轻松选择同源脊椎动物基因集，因此对于比较序列分析或分子进化研究特别有用。
Comparison of homologous genes is a major step for many studies related to genome structure, function or evolution. Similarity search programs easily find genes homologous to a given sequence. However, only very tedious manual procedures allow the retrieval of all sets of homologous genes sequenced for a given set of species. Moreover, this search often generates errors due to the complexity of data to be managed simultaneously: phylogenetic trees, alignments, taxonomy, sequences and related information. HOVERGEN helps to solve these problems by integrating all this information. HOVERGEN corresponds to GenBank sequences from all vertebrate species, with some data corrected, clarified, or completed, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments and phylogenetic trees have been calculated for each family. Sequences and related information have been structured in an ACNUC database which permits complex selections. A graphical interface has been developed to visualize and edit trees. Genes are displayed in color, according to their taxonomy. Users have directly access to all information attached to sequences and to multiple alignments simply by clicking on genes. This graphical tool gives thus a rapid and simple access to all data necessary to interpret homology relationships between genes. HOVERGEN allows the user to easily select sets of homologous vertebrate genes, and thus is particularly useful for comparative sequence analysis, or molecular evolution studies.