SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
ETH Zurich, Computer Science, Universitätstrasse 6, 8092 Zurich, Switzerland.
Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019.
The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.
同源矩阵 (OMA) 是一个主要资源，可用于将来自所有生命形式的许多物种的基因相关联。在本更新论文中，我们回顾了 OMA 管道的最新算法改进，描述了物种覆盖范围的增加（特别是在植物和早期分支的真核生物中），并在 OMA 网络浏览器中引入了几个新功能。值得注意的改进包括：(i) 用于层次同源群的可扩展、交互式查看器；(ii) 蛋白质结构域注释和基于结构域的同源群之间的链接；(iii) 检索感兴趣的一组物种的系统发育标记基因的功能；(iv) 新的同线性点图查看器；以及 (v) 对程序访问（REST API 和语义网）进行了全面检修，这将方便在计算管道中纳入 OMA 分析，并与其他生物信息学资源集成。OMA 可在 https://omabrowser.org 上免费访问。
