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URN: urn:nbn:de:kobv:517-opus-45192
URL: http://opus.kobv.de/ubp/volltexte/2010/4519/


Childs, Liam ; Nikoloski, Zoran ; May, Patrick ; Walther, Dirk

Identification and classification of ncRNA molecules using graph properties

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Kurzfassung in Deutsch

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 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.

Freie Schlagwörter (Englisch): RNA secondary structure , Noncoding RNAs , Structure prediction , Gene-expression , Structured RNAs
Institut: Institut für Biochemie und Biologie
DDC-Sachgruppe: Biowissenschaften, Biologie
Dokumentart: c Postprint
Schriftenreihe: Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, ISSN 1866-8372
Bandnummer: paper 145
Quelle: Nucleic acids research 37 (2009), 9, Art. e66, DOI: 10.1093/nar/gkp206
Sprache: Englisch
Erstellungsjahr: 2009
Publikationsdatum: 20.07.2010
Bemerkung:
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
Lizenz: Dieses Werk ist unter einer Creative Commons-Lizenz lizenziert.
Lizenz-Logo  Creative Commons - Namensnennung, Nicht kommerziell, Weitergabe zu gleichen Bedingungen 2.0 Deutschland


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