V2EX de bruijn graph

De Bruijn Graph

Definition / 定义

de Bruijn graph(德布鲁因图):一种用来表示字符串片段之间重叠关系的图结构,常用于计算机科学与生物信息学(尤其是基因组组装)。典型构造方式是:把长度为 k-1 的子串作为节点,把长度为 k 的子串(或相邻重叠关系)作为有向边,从而把“重叠拼接”问题转化为寻找欧拉路径/回路等图问题。

Pronunciation / 发音

/di brun rf/

Examples / 例句

We built a de Bruijn graph from the sequencing reads.
我们用测序读段构建了一个德布鲁因图。

By compressing non-branching paths in the de Bruijn graph, the assembler can produce longer contigs even with noisy data.
通过压缩德布鲁因图中不分叉的路径,组装器即使在噪声较大的数据下也能生成更长的 contig(连续序列片段)。

Etymology / 词源

“de Bruijn”来自荷兰数学家 Nicolaas Govert de Bruijn(尼古拉斯戈弗特德布鲁因) 的姓氏。该类图结构与他在组合数学中研究的 de Bruijn sequence(德布鲁因序列)/strong> 密切相关;后来这一思想被广泛用于字符串处理与生物序列拼接,因此形成了术语 de Bruijn graph

Related Words / 相关词

Literary Works / 文学作品举例

  • Bioinformatics Algorithms: An Active Learning Approach(Pevzner 等教材中系统讲解 de Bruijn graph 在组装中的应用)
  • Computational Molecular Biology: An Algorithmic Approach(Pevzner,讨论基因组组装相关图模型)
  • The Art of Computer Programming(Donald E. Knuth,涉及 de Bruijn 序列及相关组合结构的讨论)
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