BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
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BPhyOG：基于重叠基因的细菌系统发育全基因组推断的交互式服务器
DOI：
10.1186/1471-2105-8-266
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发表时间：
2007-07-25
影响因子：
3
通讯作者：
Lin K
中科院分区：
文献类型：
--
作者：
Luo Y;Fu C;Zhang DY;Lin K
背景细菌基因组中的重叠基因是编码序列部分或全部重叠的相邻基因对。随着序列数据的快速积累，细菌基因组中的许多OG已经被鉴定出来。事实上，这些可能被证明是所有微生物基因组的一致特征。我们以前的工作表明，OGs可以被认为是构建系统发育树的全基因组水平上的可靠标记。生物学家需要一个用于推断系统发育的在线交互网络服务器，以分析一组感兴趣的细菌基因组之间的系统发育关系。BPhyOG是一个在线交互服务器，用于根据完全测序的细菌基因组的共享重叠基因重建它们的系统发育。它提供了两种树重建方法：邻居连接法(NJ)和未加权算术平均对组法(UPGMA)。用户可以应用所需的方法来生成基于所选基因组的进化距离矩阵的系统发育树。两个基因组之间的距离由它们共享的OG对的归一化数量定义。BPhyOG还允许用户浏览用于推断系统发育关系的OG。它通过超链接为每一对OG和组成基因的特征提供了详细的注释。用户还可以检索177个基因组中已确定的每个同源OG对。它是从基因组角度分析生命树和重叠基因的有用工具。结论BPhyOG是一个有用的交互式网络服务器，可以在全基因组范围内推断用户选择的基因组之间任何潜在的进化关系。它目前包括177个完全测序的细菌基因组，包含79,855个OG对，其中的注释和同源OG对被全面整合。由注释补充的系统发育的可靠性使BPhyOG成为基因组和遗传学研究的强大网络服务器。它可以在http://cmb.bnu.edu.cn/BPhyOG上免费获得。
BackgroundOverlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.DescriptionBPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.ConclusionBPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at http://cmb.bnu.edu.cn/BPhyOG .
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DOI：
10.1073/pnas.032668599
发表时间：
2002-02-05
影响因子：
11.1
作者：
Krakauer, DC;Plotkin, JB
通讯作者：
Plotkin, JB
影响因子：
13.8
作者：
Dandekar, T;Snel, B;Bork, P
通讯作者：
Bork, P
影响因子：
3.3
作者：
Krakauer, DC
通讯作者：
Krakauer, DC
影响因子：
14.9
作者：
Fukuda, Y;Washio, T;Tomita, M
通讯作者：
Tomita, M
影响因子：
11.4
作者：
Rogozin, IB;Spiridonov, AN;Koonin, EV
通讯作者：
Koonin, EV