基于多路径广度优先搜索算法的代谢通路设计与实现
基于多路径广度优先搜索算法的代谢通路设计与实现
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国家重点研发计划项目(2018YFA0903200, 2018YFA0902900);国家自然科学基金项目(31870776);广东省科技计划项目 (2019B030316016, 2017A030313149);广州市科技计划项目(201904010337);深圳市科技创新委员会项目(KQTD2015033117210153)

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Design and Implementation of Metabolic Pathway Based on Multi-path Breadth-first Searching Algorithm
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National Key R & D Program of China (2018YFA0903200, 2018YFA0902900); National Natural Science Foundation of China (31870776), Guangdong Science and Technology Project (2019B030316016, 2017A030313149); Guangzhou Science and Technology Project (201904010337); Project of Shenzhen Science Technology and Innovation Commission (KQTD2015033117210153)

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    摘要:

    寻找从底物到产物的可行代谢通路是代谢工程设计中的核心环节。针对复杂代谢网络中代谢 通路不唯一的情况以及传统 K 条最短路径(K-Shortest Path,KSP)算法效率低的问题,该文通过对传统 KSP 算法的优化,引入关键边概念以减少非必要的重复计算;搭建代谢通路设计 Web 平台,使用并行 计算方式提升了算法运算性能。最终,通过引入代谢网络图,对改进 KSP 算法的多路径搜索效率进行 验证,结果显示较传统 KSP 算法有 5~9 倍的性能提升。

    Abstract:

    To find possible reactions that exist in metabolic networks is essential for metabolic engineering. The K-shortest path (KSP) algorithm is a traditional method that is usually used to identify alternative metabolic pathways. To improve the computation efficiency of conventional KSP method, an efficient KSP-based searching method is proposed in this paper. The basic idea is to introduce the critical edge to reduce the redundant calculation. A web-platform is constructed to design metabolic pathways. The parallel computing technique is introduced to improve the computing efficiency. The proposed method is validated on the KEGG metabolic pathways map, and the results show that the proposed method improve the computation efficiency by 5-9 times, compared with the traditional KSP algorithm.

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引文格式
黄祖成,沈梦圆,侯至丞,TOKUYASU Taku Andrew,蒙海林.基于多路径广度优先搜索算法的代谢通路设计与实现 [J].集成技术,2021,10(5):72-79

Citing format
HUANG Zucheng, SHEN Mengyuan, HOU Zhicheng, TOKUYASU Taku Andrew, MENG Hailin. Design and Implementation of Metabolic Pathway Based on Multi-path Breadth-first Searching Algorithm[J]. Journal of Integration Technology,2021,10(5):72-79

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  • 在线发布日期: 2021-09-15
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