gapseq:细菌代谢途径的知情预测和准确代谢模型的重建。

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2021-03-10 DOI:10.1186/s13059-021-02295-1
Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
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引用次数: 0

摘要

微生物的基因组尺度代谢模型是根据生物基因型预测表型的强大框架。人工重建费时费力,而自动重建往往不能再现已知的代谢过程。在这里,我们介绍一种新的工具 gapseq ( https://github.com/jotech/gapseq ) ,它可以预测代谢途径,并利用一个经过整理的反应数据库和一种新颖的填补空白算法自动重建微生物代谢模型。根据科学文献和 14931 种细菌表型的实验数据,我们证明了 gapseq 在预测微生物群落中的酶活性、碳源利用、发酵产物和代谢相互作用方面优于最先进的工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.

Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.

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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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