Liftoff: an accurate gene annotation mapping tool
Liftoff: an accurate gene annotation mapping tool
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DOI：
10.1101/2020.06.24.169680
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发表时间：
2020-06
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通讯作者：
Alaina Shumate;S. Salzberg
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作者：
Alaina Shumate;S. Salzberg
DNA测序技术和计算方法的改进导致许多物种的高质量基因组组装的创建大幅增加。为了了解这些基因组的生物学特性，对基因特征和其他功能元件的注释是必不可少的；然而，对于大多数物种，只有参考基因组被很好地注释。注释新的或改进的基因组组合的一种策略是从先前注释的参考基因组中绘制或“抬起”基因。在这里，我们描述Liftoff，一种新的基因组注释提升工具，能够在相同或密切相关的物种的两个组装之间定位基因。Liftoff将参考基因组中的基因与目标基因组比对，并在保留每个外显子、转录本和基因结构的同时，找到最大限度地提高序列一致性的图谱。结果表明，Liftoff可以准确地绘制出99.9%的人类参考基因组之间的基因图谱，平均序列一致性为99.9%。通过成功地将98.4%的人类蛋白质编码基因提升到具有98.7%序列一致性的黑猩猩基因组组装中，Liftoff还可以绘制跨物种基因图谱。Liftoff的源代码可从https://github.com/agshumate/Liftoff获得
Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.4% of human protein-coding genes to a chimpanzee genome assembly with 98.7% sequence identity. Availability The source code for Liftoff is available at https://github.com/agshumate/Liftoff