{"title":"非编码 RNA 的大偏差原理和进化多重结构比对","authors":"Brandon Legried","doi":"arxiv-2405.14904","DOIUrl":null,"url":null,"abstract":"Non-coding RNA are functional molecules that are not translated into\nproteins. Their function comes as important regulators of biological function.\nBecause they are not translated, they need not be as stable as other types of\nRNA. The TKF91 Structure Tree from Holmes 2004 is a probability model that\neffectively describes correlated substitution, insertion, and deletion of base\npairs, and found to have some worth in understanding dynamic folding patterns.\nIn this paper, we provide a new probabilistic analysis of the TKF91 Structure\nTree. Large deviation principles on stem lengths, helix lengths, and tree size\nare proved. Additionally, we give a new alignment procedure that constructs\naccurate sequence and structural alignments for sequences with low identity for\na dense enough phylogeny.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"237 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Large deviation principles and evolutionary multiple structure alignment of non-coding RNA\",\"authors\":\"Brandon Legried\",\"doi\":\"arxiv-2405.14904\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Non-coding RNA are functional molecules that are not translated into\\nproteins. Their function comes as important regulators of biological function.\\nBecause they are not translated, they need not be as stable as other types of\\nRNA. The TKF91 Structure Tree from Holmes 2004 is a probability model that\\neffectively describes correlated substitution, insertion, and deletion of base\\npairs, and found to have some worth in understanding dynamic folding patterns.\\nIn this paper, we provide a new probabilistic analysis of the TKF91 Structure\\nTree. Large deviation principles on stem lengths, helix lengths, and tree size\\nare proved. Additionally, we give a new alignment procedure that constructs\\naccurate sequence and structural alignments for sequences with low identity for\\na dense enough phylogeny.\",\"PeriodicalId\":501219,\"journal\":{\"name\":\"arXiv - QuanBio - Other Quantitative Biology\",\"volume\":\"237 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-05-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"arXiv - QuanBio - Other Quantitative Biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/arxiv-2405.14904\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Other Quantitative Biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2405.14904","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Large deviation principles and evolutionary multiple structure alignment of non-coding RNA
Non-coding RNA are functional molecules that are not translated into
proteins. Their function comes as important regulators of biological function.
Because they are not translated, they need not be as stable as other types of
RNA. The TKF91 Structure Tree from Holmes 2004 is a probability model that
effectively describes correlated substitution, insertion, and deletion of base
pairs, and found to have some worth in understanding dynamic folding patterns.
In this paper, we provide a new probabilistic analysis of the TKF91 Structure
Tree. Large deviation principles on stem lengths, helix lengths, and tree size
are proved. Additionally, we give a new alignment procedure that constructs
accurate sequence and structural alignments for sequences with low identity for
a dense enough phylogeny.