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Automated generation of genome-scale metabolic draft reconstructions based on KEGG

机译:基于KEGG的基因组规模代谢草案重建的自动生成

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摘要

BackgroundConstraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale metabolic network reconstruction. The creation, further development, and application of such networks is a growing field of research thanks to a plethora of readily accessible computational tools. While the majority of studies are focused on single-species analyses, typically of a microbe, the computational study of communities of organisms is gaining attention. Similarly, reconstructions that are unified for a multi-cellular organism have gained in popularity. Consequently, the rapid generation of genome-scale metabolic reconstructed networks is crucial. While multiple web-based or stand-alone tools are available for automated network reconstruction, there is, however, currently no publicly available tool that allows the swift assembly of draft reconstructions of community metabolic networks and consolidated metabolic networks for a specified list of organisms.
机译:背景技术基于约束的建模是一种广泛使用且功能强大的方法,用于评估生物的代谢表型和能力。所有此类建模的起点和基石都是基因组规模的代谢网络重建。由于大量易于使用的计算工具,此类网络的创建,进一步开发和应用是一个不断发展的研究领域。尽管大多数研究都集中在单一物种分析(通常是微生物)上,但是生物群落的计算研究正受到关注。类似地,针对多细胞生物而统一的重建已经普及。因此,快速生成基因组规模的代谢重建网络至关重要。尽管可以使用多种基于Web的工具或独立工具来进行自动化网络重建,但是,目前尚没有公开可用的工具,该工具可以针对特定生物列表快速组装社区代谢网络和合并代谢网络的草图。

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