SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
ETH Zurich, Department of Computer Science, Zurich, Switzerland.
Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308.
The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.
在比较基因组学和分子进化的许多分析中，识别来自同一祖先的不同物种中的直系同源基因（orthologs-genes）是前提。为此，人们已经设计了许多算法和资源，但对它们进行基准测试和解释却困难重重（需要在公共输入数据集上进行比较，缺乏真实情况，调用直系同源基因的计算成本）。为了解决这个问题，寻找直系同源基因联盟维护了一个蛋白质组参考集，并提供了一个用于连续直系同源基因基准测试的网络服务器（http://orthology.benchmarkservice.org）。此外，来自公共基准提交的共识直系同源基因调用结果也可以在联盟基因组资源网站上获得，该网站是由美国国立卫生研究院资助的模式生物数据库的联合门户。
