基于贪心策略的多毒株病毒全长参考基因组组装算法  

Full-length Reference Genome Assembly Algorithm ofMulti-strain Virus Based on Greedy Strategy

作　　者：高梓煜 赵瑾 GAO Zi-yu;ZHAO Jin(School of Computer Science and Technology,Qingdao University,Qingdao 266071,China)

机构地区：[1]青岛大学计算机科学技术学院,青岛266071

出　　处：《青岛大学学报(自然科学版)》2025年第1期24-29,共6页Journal of Qingdao University(Natural Science Edition)

基　　金：国家自然科学基金(批准号:62202251)资助;山东省自然科学基金(批准号:ZR2022QF133)资助。

摘　　要：病毒基因组具有高度遗传异质性,传统组装方法的拼装结果存在片段化问题。为此,提出了一种基于贪心策略的方法(RK-Virus),通过k-mer提取、选取种子、序列扩展等步骤构建全长参考基因组。实验结果表明,RK-Virus拼装出的Contig数量始终为1,解决了现有算法的片段化问题,在两个数据集上每100 kbp的错误数平均减少了25.2%。Viral genomes have a high degree of genetic heterogeneity,causing issues of fragmentation in traditional assembly methods.To tackle this problem,a method named RK-Virus was proposed that utilized a greedy strategy to build a full-length reference genome through steps such as k-mer extraction,seed selection,and sequence extension.The experimental results show that RK-Virus consistently generates a single Contig,overcoming the fragmentation problem of existing algorithms.Moreover,it reduces the average number of errors per 100 kbp by 25.2%on both two datasets.

关 键 词：参考基因组组装 病毒基因组 计算生物学 

分 类 号：TP391[自动化与计算机技术—计算机应用技术]