{"title":"Counting Distinguishable RNA Secondary Structures.","authors":"Masaru Nakajima, Andrew D Smith","doi":"10.1089/cmb.2022.0501","DOIUrl":null,"url":null,"abstract":"<p><p>RNA secondary structures are essential abstractions for understanding spacial folding behaviors of those macromolecules. Many secondary structure algorithms involve a common dynamic programming setup to exploit the property that secondary structures can be decomposed into substructures. Dirks et al. noted that this setup cannot directly address an issue of distinguishability among secondary structures, which arises for classes of sequences that admit nontrivial symmetry. Circular sequences are among these. We examine the problem of counting distinguishable secondary structures. Drawing from elementary results in group theory, we identify useful subsets of secondary structures. We then extend an algorithm due to Hofacker et al. for computing the sizes of these subsets. This yields a cubic-time algorithm to count distinguishable structures compatible with a given circular sequence. Furthermore, this general approach may be used to solve similar problems for which the RNA structures of interest involve symmetries.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":null,"pages":null},"PeriodicalIF":1.4000,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1089/cmb.2022.0501","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/10/9 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
RNA secondary structures are essential abstractions for understanding spacial folding behaviors of those macromolecules. Many secondary structure algorithms involve a common dynamic programming setup to exploit the property that secondary structures can be decomposed into substructures. Dirks et al. noted that this setup cannot directly address an issue of distinguishability among secondary structures, which arises for classes of sequences that admit nontrivial symmetry. Circular sequences are among these. We examine the problem of counting distinguishable secondary structures. Drawing from elementary results in group theory, we identify useful subsets of secondary structures. We then extend an algorithm due to Hofacker et al. for computing the sizes of these subsets. This yields a cubic-time algorithm to count distinguishable structures compatible with a given circular sequence. Furthermore, this general approach may be used to solve similar problems for which the RNA structures of interest involve symmetries.
期刊介绍:
Journal of Computational Biology is the leading peer-reviewed journal in computational biology and bioinformatics, publishing in-depth statistical, mathematical, and computational analysis of methods, as well as their practical impact. Available only online, this is an essential journal for scientists and students who want to keep abreast of developments in bioinformatics.
Journal of Computational Biology coverage includes:
-Genomics
-Mathematical modeling and simulation
-Distributed and parallel biological computing
-Designing biological databases
-Pattern matching and pattern detection
-Linking disparate databases and data
-New tools for computational biology
-Relational and object-oriented database technology for bioinformatics
-Biological expert system design and use
-Reasoning by analogy, hypothesis formation, and testing by machine
-Management of biological databases