App. Res. of Comp. Accepted Paper
Vol. 41, 2024 No. 8

Position filtering method for tandem repeat sequence alignment

Wen Huaming1,2
Xu Yun1,2
Yang Jinbao3
1. School of Computer Science & Technology, University of Science & Technology of China, Hefei 230027, China
2. Key Laboratory of High Performance Computing of Anhui Province, Hefei 230027, China
3. College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
DOI: 10.19734/j.issn.1001-3695.2023.12.0614

Abstract

Tandem repeat sequences present challenges in genome assembly due to the difficulty in resolving their repetitive units and the uncertainty surrounding their copy numbers. During sequence alignment, the high similarity between repeated units and the ambiguity in copy numbers often result in multiple candidate positions. The challenge 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. However, these methods overlook the distinctive characteristics of tandem repeat sequences when selecting seeds. To tackle the problem, a position filtering method for tandem repeat sequence alignment is proposed, which filters alignment results by calculating the similarity of rare kmer sequences. Additionally, a strategy of merging rare kmers is implemented to expedite computation, coupled with a fuzzy search based on edit distance to enhance filtering information density. Experimental results demonstrate that this approach 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.

Foundation Support

国家自然科学基金面上项目(61672480)
国家外专局111引智计划资助项目(BP0719016)

Publish Information

DOI: 10.19734/j.issn.1001-3695.2023.12.0614
Publish at: Application Research of Computers Accepted Paper, Vol. 41, 2024 No. 8

Publish History

[2024-03-07] Accepted Paper

Cite This Article

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 (8). (2024-04-10). https://doi.org/10.19734/j.issn.1001-3695.2023.12.0614. (Wen Huaming, Xu Yun, Yang Jinbao. Position filtering method for tandem repeat sequence alignment [J]. Application Research of Computers, 2024, 41 (8). (2024-04-10). https://doi.org/10.19734/j.issn.1001-3695.2023.12.0614. )

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  • Application Research of Computers Monthly Journal
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    CN  51-1196/TP

Application Research of Computers, founded in 1984, is an academic journal of computing technology sponsored by Sichuan Institute of Computer Sciences under the Science and Technology Department of Sichuan Province.

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