OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
复制标题
DOI：
10.1093/nar/gkn240
复制
发表时间：
2008-07-01
影响因子：
14.9
通讯作者：
Lu CL
中科院分区：
文献类型：
--
作者：
Jiang LW;Lin KL;Lu CL
OGtree是一个基于网络的构建原核生物基因组树的工具，它结合了原核生物全基因组中的基因含量和基因顺序。重叠基因（overlapping gene，OG）是指编码序列部分或全部重叠的相邻基因。事实上，OG在微生物基因组中普遍存在，并且在物种之间比非OG更保守。基于这些特性，已经表明，OG可以作为更好的系统发育特征比非OG之间的微生物基因组的进化关系重建。OGtree将原核生物基因组的登录号作为其输入。然后，它从国家生物技术信息中心下载它们的完整基因组，并识别每个基因组中的OG及其在其他基因组中的同源性OG。接下来，OGtree基于它们的OG内容和正交OG顺序的组合来计算每对输入基因组之间的重复基因距离。最后，它利用基于距离的方法建立树输入的原核基因组的基因组树，根据它们的成对OG距离。OGtree可在http://bioalgorithm.life.nctu.edu.tw/OGtree/在线获得。
OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. The overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, OGs are ubiquitous in microbial genomes and more conserved between species than non-OGs. Based on these properties, it has been suggested that OGs can serve as better phylogenetic characters than non-OGs for reconstructing the evolutionary relationships among microbial genomes. OGtree takes the accession numbers of prokaryotic genomes as its input. It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes. Next, OGtree computes an overlapping-gene distance between each pair of input genomes based on a combination of their OG content and orthologous OG order. Finally, it utilizes distance-based methods of building tree to reconstruct the genome trees of input prokaryotic genomes according to their pairwise OG distance. OGtree is available online at http://bioalgorithm.life.nctu.edu.tw/OGtree/.
登录
查看更多内容
影响因子：
30.8
作者：
Snel, B;Bork, P;Huynen, MA
通讯作者：
Huynen, MA
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
影响因子：
5.8
作者：
Sankoff, D
通讯作者：
Sankoff, D