重建器:一种与COBRApy兼容的工具,用于自动化基因组规模的代谢网络重建,并以节的流量为基础填补空白
Matthew L Jenior1, Emma M Glass1, Jason A Papin1,2,3
1Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States.
Bioinformatics (Oxford, England)
|June 6, 2023
概括
重建器是一个用户友好的工具,用于生成高质量的基因组规模代谢网络重建 (GENREs). 它与COBRApy和ModelSEED集成,有助于研究细菌代谢.
科学领域:
- 系统生物学 系统生物学
- 代谢工程是代谢工程.
- 计算生物学 计算生物学
背景情况:
- 基因组规模的代谢网络重建 (GENREs) 对于细胞代谢的分析至关重要.
- 现有的自动化GENRE生成工具往往由于集成不良,策划功能有限,用户不友好和质量低的输出而受到影响.
研究的目的:
- 介绍 Reconstructor,一个新的,用户友好的软件工具,旨在克服现有的 GENRE 生成方法的局限性.
- 为生成高质量的代谢重建草案提供一个与COBRApy兼容的平台.
主要方法:
- 重建器从蛋白质序列,BLASTp输出或现有的SBML文件中生成系统生物学标记语言 (SBML) 的GENREs.
- 它使用标准化命名惯例确保与ModelSEED生物化学数据库的一致性.
- 基于节的缺口填补技术被纳入,以提高重建质量.
主要成果:
- 重建器制作高质量的草稿 GENREs 具有一致的命名体系.
- 该工具成功地捕捉了细菌菌株,物种和更高分类层的代谢差异.
- 在用于生物发现的细菌代谢网络重建中证明了实用性.
结论:
- 重建器为生成高质量的GENREs提供了一个用户友好和有效的解决方案.
- 该工具促进了功能代谢的探索,并有助于生物发现,特别是细菌.
- 重建器为研究人员提高了代谢网络重建的可访问性和质量.
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