Chao Kuan-Hao, Heinz Jakob M, Hoh Celine, Mao Alan, Shumate Alaina, Pertea Mihaela, Salzberg Steven L
Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.
Genome Res. 2025 Feb 14;35(2):311-325. doi: 10.1101/gr.279620.124.
As the number and variety of assembled genomes continue to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species. LiftOn's protein-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies when they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honeybee, rice, and It can further map annotation effectively across species pairs as far apart as mouse and rat or and .
随着已组装基因组的数量和种类不断增加，注释基因组的数量却滞后了，尤其是对于真核生物而言。基于DNA的映射工具有助于应对这一挑战，但它们只能在亲缘关系密切的物种之间转移注释。在此，我们介绍LiftOn，这是一种基于同源性的软件工具，它整合了DNA和蛋白质比对，以提高基因组规模注释的准确性，并允许在亲缘关系相对较远的物种之间进行映射。LiftOn以蛋白质为中心的算法考虑了两种比对类型，选择最佳开放阅读框，解析重叠基因座，并在存在额外基因拷贝时找到它们。正如我们在人类、小鼠、蜜蜂、水稻以及……上所展示的，LiftOn能够在代表同一物种成员的基因组之间可靠地转移注释。它还能进一步有效地跨物种对进行注释映射，比如小鼠和大鼠或……和……之间。
