Identification and classification of ncRNA molecules using graph properties
- The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particularThe study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets.…
Author details: | Liam H. Childs, Zoran NikoloskiORCiDGND, Patrick May, Dirk Walther |
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URN: | urn:nbn:de:kobv:517-opus-45192 |
Publication series (Volume number): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (paper 145) |
Publication type: | Postprint |
Language: | English |
Publication year: | 2009 |
Publishing institution: | Universität Potsdam |
Release date: | 2010/07/20 |
Tag: | Gene-expression; Noncoding RNAs; RNA secondary structure; Structure prediction; Structured RNAs |
Source: | Nucleic acids research 37 (2009), 9, Art. e66, DOI: 10.1093/nar/gkp206 |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
License (German): | Creative Commons - Namensnennung, Nicht kommerziell, Weitergabe zu gleichen Bedingungen 2.0 Deutschland |
External remark: | The article was originally published by Oxford University Press: Nucleic Acids Research. - 37 (2009), 9, Art. e66 (12 S.) ISSN 0305-1048 DOI 10.1093/nar/gkp206 |