计算机应用研究2024，Vol.41Issue(7)：2160-2164,5.DOI:10.19734/j.issn.1001-3695.2023.12.0614
串联重复序列比对的位置筛选方法
Position filtering method for tandem repeat sequence alignment
摘要
Abstract
Tandem repeat sequences are difficult part in genome construction,due to the high similarity between repeated units and the ambiguity in copy numbers,it often result in multiple candidate positions during sequence alignment.The chal-lenge lies in rapidly and accurately filtering out the correct alignment positions.Existing methods address this issue by using seeds(short sequences selected from sequencing fragments)to locate and extend candidate alignment positions,but overlook the distinctive characteristics of tandem repeat sequences when selecting seeds.To tackle the problem,this paper proposed a position filtering method for tandem repeat sequence alignment,which filtered alignment results by calculating the similarity of rare kmer sequences.Additionally,it implemented a strategy of merging rare kmers to expedite computation,coupled with a fuzzy search based on edit distance to enhance filtering information density.Experimental results demonstrate that this ap-proach improves both the recall and accuracy of alignment results on simulated datasets while achieving approximately a 2-fold increase in computational speed compared to existing methods,with notable parallel acceleration effects.关键词
串联重复/单分子实时测序/序列比对/种子-扩展法Key words
tandem repeat/single molecule real-time sequencing/sequence alignment/seed-and-extend method分类
信息技术与安全科学引用本文复制引用
温华铭,徐云,杨金宝..串联重复序列比对的位置筛选方法[J].计算机应用研究,2024,41(7):2160-2164,5.基金项目
国家自然科学基金面上项目(61672480) （61672480）
国家外专局111引智计划资助项目(BP0719016) （BP0719016）
