{"title":"H-ACO with Consecutive Bases Pairing Constraint for Designing DNA Sequences","authors":"Xuwei Yang, Donglin Zhu, Can Yang, Changjun Zhou","doi":"10.1007/s12539-024-00614-1","DOIUrl":null,"url":null,"abstract":"<p>DNA computing is a novel computing method that does not rely on traditional computers. The design of DNA sequences is a crucial step in DNA computing, and the quality of the sequence design directly affects the results of DNA computing. In this paper, a new constraint called the consecutive base pairing constraint is proposed to limit specific base pairings in DNA sequence design. Additionally, to improve the efficiency and capability of DNA sequence design, the Hierarchy-ant colony (H-ACO) algorithm is introduced, which combines the features of multiple algorithms and optimizes discrete numerical calculations. Experimental results show that the H-ACO algorithm performs well in DNA sequence design. Finally, this paper compares a series of constraint values and NUPACK simulation data with previous design results, and the DNA sequence set designed in this paper has more advantages.</p><h3 data-test=\"abstract-sub-heading\">Graphical Abstract</h3>\n","PeriodicalId":13670,"journal":{"name":"Interdisciplinary Sciences: Computational Life Sciences","volume":"5 1","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Interdisciplinary Sciences: Computational Life Sciences","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s12539-024-00614-1","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
DNA computing is a novel computing method that does not rely on traditional computers. The design of DNA sequences is a crucial step in DNA computing, and the quality of the sequence design directly affects the results of DNA computing. In this paper, a new constraint called the consecutive base pairing constraint is proposed to limit specific base pairings in DNA sequence design. Additionally, to improve the efficiency and capability of DNA sequence design, the Hierarchy-ant colony (H-ACO) algorithm is introduced, which combines the features of multiple algorithms and optimizes discrete numerical calculations. Experimental results show that the H-ACO algorithm performs well in DNA sequence design. Finally, this paper compares a series of constraint values and NUPACK simulation data with previous design results, and the DNA sequence set designed in this paper has more advantages.
DNA 计算是一种不依赖传统计算机的新型计算方法。DNA 序列的设计是 DNA 计算的关键步骤，序列设计的质量直接影响 DNA 计算的结果。本文提出了一种名为连续碱基配对约束的新约束，以限制 DNA 序列设计中的特定碱基配对。此外，为了提高 DNA 序列设计的效率和能力，本文引入了层次-蚁群（H-ACO）算法，该算法结合了多种算法的特点，优化了离散数值计算。实验结果表明，H-ACO 算法在 DNA 序列设计中表现良好。最后，本文将一系列约束值和 NUPACK 仿真数据与之前的设计结果进行了比较，结果表明本文设计的 DNA 序列集更具优势。
期刊介绍：
Interdisciplinary Sciences--Computational Life Sciences aims to cover the most recent and outstanding developments in interdisciplinary areas of sciences, especially focusing on computational life sciences, an area that is enjoying rapid development at the forefront of scientific research and technology.
The journal publishes original papers of significant general interest covering recent research and developments. Articles will be published rapidly by taking full advantage of internet technology for online submission and peer-reviewing of manuscripts, and then by publishing OnlineFirstTM through SpringerLink even before the issue is built or sent to the printer.
The editorial board consists of many leading scientists with international reputation, among others, Luc Montagnier (UNESCO, France), Dennis Salahub (University of Calgary, Canada), Weitao Yang (Duke University, USA). Prof. Dongqing Wei at the Shanghai Jiatong University is appointed as the editor-in-chief; he made important contributions in bioinformatics and computational physics and is best known for his ground-breaking works on the theory of ferroelectric liquids. With the help from a team of associate editors and the editorial board, an international journal with sound reputation shall be created.
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