ADFinder：利用 NGS 高通量测序数据进行精确的可编程 DNA 消除检测。

ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data.

机构信息

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.

出版信息

Bioinformatics. 2020 Jun 1;36(12):3632-3636. doi: 10.1093/bioinformatics/btaa226.

DOI:10.1093/bioinformatics/btaa226

PMID:32246828

Abstract

MOTIVATION

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.

RESULTS

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.

AVAILABILITY AND IMPLEMENTATION

The source codes and manual of ADFinder are available in our GitHub website: https://github.com/weibozheng/ADFinder.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

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。