Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
Department of Mechanic and Electronic Engineering, Beijing Information Science & Technology University, Beijing 100192, China.
Bioinformatics. 2020 Jun 1;36(12):3632-3636. doi: 10.1093/bioinformatics/btaa226.
Programmed DNA elimination (PDE) plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific for the detection of DNA splicing events is scarce. In this paper, we describe Accurate Deletion Finder (ADFinder), an efficient detector of PDEs using high-throughput sequencing data. ADFinder can predict PDEs with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location and calculate the frequency for each splicing event. This software will facilitate research of PDEs and all down-stream analyses.
By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila, we prove that ADFinder is effective in predicting large scale PDEs.
The source codes and manual of ADFinder are available in our GitHub website: https://github.com/weibozheng/ADFinder.
Supplementary data are available at Bioinformatics online.
程序性 DNA 消除 (PDE) 在从单细胞纤毛虫到多细胞线虫等各种生物体的生殖系和体细胞基因组之间的转变中起着至关重要的作用。然而，专门用于检测 DNA 剪接事件的软件却很少。在本文中，我们描述了 Accurate Deletion Finder (ADFinder)，这是一种使用高通量测序数据检测 PDE 的高效探测器。ADFinder 可以预测具有相对较低测序覆盖率的 PDE，检测同一基因组位置中的多个替代剪接形式，并计算每个剪接事件的频率。该软件将促进 PDE 及其所有下游分析的研究。
通过分析 Oxytricha trifallax 和 Tetrahymena thermophila 的两个微核基因组中的全基因组 DNA 剪接事件，我们证明了 ADFinder 有效地预测了大规模的 PDE。
ADFinder 的源代码和手册可在我们的 GitHub 网站上获得：https://github.com/weibozheng/ADFinder。
补充数据可在 Bioinformatics 在线获得。
