ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa
ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa
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DOI：
10.1093/molbev/msy226
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发表时间：
2019-03-01
影响因子：
10.7
通讯作者：
Satoh, Noriyuki
中科院分区：
文献类型：
--
作者：
Inoue, Jun;Satoh, Noriyuki
鉴定编码基因的直系同源或旁系同源关系是比较基因组学各个方面的基础。为了准确鉴定高度多样化的两侧对称谱系中的直系同源物，考虑到数百万年来基因的复杂历史，精确估计基因树是必不可少的。通过估计基因树，直向同源物可以被识别为一个直向群的成员，直向群是从所有被考虑的物种的最后一个共同祖先中的单个基因传下来的一组基因。除了与给定的物种树进行比较之外，有目的的分类取样还增加了基因树估计和正群鉴定的准确性。虽然一些主要的系统发育关系的bilaterians逐渐被解开，分散在不同的网络数据库中公布的基因组数据正在成为一个显着的障碍，以确定orthogroups与适当的分类采样。通过整合基因组计划中预测的250多个后生动物基因模型，我们开发了一个名为ORTHOSCOPE的网络工具来识别主要两侧体谱系中特定蛋白质编码基因的正群。ORTHOSCOPE允许用户采用特定分子的几个序列和用户指定的物种树中包含的广泛接受的节点作为查询，并基于估计基因树的拓扑结构和节点支持值来评估估计的正群的可靠性。在140 s内完成了对36例双侧性脑梗死患者数据的检验分析。ORTHOSCOPE结果可用于评估使用基因组规模数据由其他独立程序鉴定的直系同源物。ORTHOSCOPE可在https://www.orthoscope.jp或https://github.com/jun-inoue/orthoscope上免费获取（最后一次访问日期为2018年12月28日）。
Identification of orthologous or paralogous relationships of coding genes is fundamental to all aspects of comparative genomics. For accurate identification of orthologs among deeply diversified bilaterian lineages, precise estimation of gene trees is indispensable, given the complicated histories of genes over millions of years. By estimating gene trees, orthologs can be identified as members of an orthogroup, a set of genes descended from a single gene in the last common ancestor of all the species being considered. In addition to comparisons with a given species tree, purposeful taxonomic sampling increases the accuracy of gene tree estimation and orthogroup identification. Although some major phylogenetic relationships of bilaterians are gradually being unraveled, the scattering of published genomic data among separate web databases is becoming a significant hindrance to identification of orthogroups with appropriate taxonomic sampling. By integrating more than 250 metazoan gene models predicted in genome projects, we developed a web tool called ORTHOSCOPE to identify orthogroups of specific protein-coding genes within major bilaterian lineages. ORTHOSCOPE allows users to employ several sequences of a specific molecule and broadly accepted nodes included in a user-specified species tree as queries and to evaluate the reliability of estimated orthogroups based on topologies and node support values of estimated gene trees. A test analysis using data from 36 bilaterians was accomplished within 140s. ORTHOSCOPE results can be used to evaluate orthologs identified by other stand-alone programs using genome-scale data. ORTHOSCOPE is freely available at https://www.orthoscope.jp or https://github.com/jun-inoue/orthoscope (last accessed December 28, 2018).