Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.
Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
F1000Res. 2024 Apr 29;11:1230. doi: 10.12688/f1000research.124059.2. eCollection 2022.
In 2020 we published Liftoff, which was the first standalone tool specifically designed for transferring gene annotations between genome assemblies of the same or closely related species. While the gene content is expected to be very similar in closely related genomes, the differences may be biologically consequential, and a computational method to extract all gene-related differences should prove useful in the analysis of such genomes. Here we present LiftoffTools, a toolkit to automate the detection and analysis of gene sequence variants, synteny, and gene copy number changes. We provide a description of the toolkit and an example of its use comparing genes mapped between two human genome assemblies.
2020 年，我们发布了 Liftoff，这是第一个专门设计用于在相同或密切相关物种的基因组组装之间转移基因注释的独立工具。虽然密切相关的基因组中的基因内容预计非常相似，但这些差异可能具有生物学意义，因此提取所有与基因相关的差异的计算方法应该有助于分析此类基因组。在这里，我们介绍了 LiftoffTools，这是一个用于自动化检测和分析基因序列变体、基因同线性和基因拷贝数变化的工具包。我们提供了该工具包的描述，并提供了一个使用示例，比较了两个人类基因组组装之间映射的基因。
