Division of Microbiology, National Center for Toxicological Research (NCTR)/U.S. FDA, Jefferson, AR, 72079, USA.
NCTR/U.S. FDA, Jefferson, AR, 72211, USA.
BMC Bioinformatics. 2020 Apr 29;21(1):160. doi: 10.1186/s12859-020-3473-2.
Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner.
CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences.
CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.
细胞色素 P450 单加氧酶（简称 CYP 或 P450）是一种广泛存在于所有生物界的血红素蛋白，在细胞内代谢中起着核心作用，尤其是在药物和外源化合物的代谢中。基因组测序的飞速发展给研究人员带来了一系列新的挑战和问题，例如系统地研究所有生物界的 CYP 从鉴定、分类到泛 CYP 组分析。这种研究需要一个能够及时处理大量测序数据的自动化工具。
CYPminer 是用 Python 语言开发的，用于快速、全面地分析来自所有生物界基因组的 CYP。CYPminer 由两个程序组成：i）生成基因组-CYP 矩阵 (GCM)，列出基因组中所有 CYP 的出现情况，ii）对 GCM 进行分析和可视化，包括泛 CYP 组（泛和核心 CYP 组）、CYP 共同出现网络、CYP 云以及基因组聚类数据。用来自真菌和细菌基因组序列的三个数据集评估了 CYPminer 的性能。
CYPminer 完成了来自所有生物界的大规模基因组的 CYP 分析，这使得对 CYP 进行系统的基因组注释和比较分析成为可能。CYPminer 也可以很容易地扩展和适应更广泛的用途。
