Vieira Mourato Beatriz, Haubold Bernhard
Research Group Bioinformatics, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
Comput Struct Biotechnol J. 2025 Feb 27;27:843-850. doi: 10.1016/j.csbj.2025.02.025. eCollection 2025.
Unique genomic regions are of particular interest in two scenarios: When extracted from a single mammalian target genome, they are highly enriched for developmental genes. When extracted from target genomes compared to closely related neighbor genomes, they are highly enriched for diagnostic markers. Despite their biological importance and potential economic value, unique regions remain difficult to detect from whole genome sequences. In this review we survey three efficient programs for the detection of unique regions at scale, genmap, macle, and fur. We explain these programs and demonstrate their application by analyzing simulated and real data. Example scripts for searching for unique regions are available from the Github repository evolbioinf/sure as part of a detailed tutorial.
当从单个哺乳动物目标基因组中提取时，它们高度富集发育基因。当从目标基因组与密切相关的邻近基因组进行比较时提取，它们高度富集诊断标记。尽管它们具有生物学重要性和潜在的经济价值，但从全基因组序列中检测独特区域仍然很困难。在本综述中，我们调查了三种大规模检测独特区域的有效程序，即genmap、macle和fur。我们解释这些程序，并通过分析模拟数据和真实数据来展示它们的应用。作为详细教程的一部分，可从Github仓库evolbioinf/sure获得搜索独特区域的示例脚本。
