Reference : Identification and classification of ncRNA molecules using graph properties.
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Identification and classification of ncRNA molecules using graph properties.
Childs, Liam [> >]
Nikoloski, Zoran [> >]
May, Patrick mailto [Max Planck Institute for Molecular Plant Physiology > Bioinformatics]
Walther, Dirk [> >]
Nucleic Acids Research
Yes (verified by ORBilu)
[en] Algorithms ; Computer Graphics ; Nucleic Acid Conformation ; RNA, Untranslated/chemistry/classification ; Sequence Alignment ; Sequence Analysis, RNA ; Software
[en] 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.

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