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Software Technology Research
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App. Res. of Comp. Printed Article
Vol. 41, 2024 No. 7
2160-2164

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 Perfor-mance 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 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 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, 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 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 Printed Article, Vol. 41, 2024 No. 7
Section: Software Technology Research
Pages: 2160-2164
Serial Number: 1001-3695(2024)07-033-2160-05

Publish History

[2024-03-07] Accepted Paper
[2024-07-05] Printed Article

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 (7): 2160-2164. (Wen Huaming, Xu Yun, Yang Jinbao. Position filtering method for tandem repeat sequence alignment [J]. Application Research of Computers, 2024, 41 (7): 2160-2164. )

About the Journal

  • Application Research of Computers Monthly Journal
  • Journal ID ISSN 1001-3695
    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.

Aiming at the urgently needed cutting-edge technology in this discipline, Application Research of Computers reflects the mainstream technology, hot technology and the latest development trend of computer application research at home and abroad in a timely manner. The main contents of the journal include high-level academic papers in this discipline, the latest scientific research results and major application results. The contents of the columns involve new theories of computer discipline, basic computer theory, algorithm theory research, algorithm design and analysis, blockchain technology, system software and software engineering technology, pattern recognition and artificial intelligence, architecture, advanced computing, parallel processing, database technology, computer network and communication technology, information security technology, computer image graphics and its latest hot application technology.

Application Research of Computers has many high-level readers and authors, and its readers are mainly senior and middle-level researchers and engineers engaged in the field of computer science, as well as teachers and students majoring in computer science and related majors in colleges and universities. Over the years, the total citation frequency and Web download rate of Application Research of Computers have been ranked among the top of similar academic journals in this discipline, and the academic papers published are highly popular among the readers for their novelty, academics, foresight, orientation and practicality.

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