DNA carries and passes the genetic information with nucleotides sequences, but in some virus RNA does the job instead of DNA. In addition, the 3D structure of RNA, RNA motif, shows more various roles in cellular functions. It means that only with sequence information we cannot fully understand the RNA roles and functions.
Detecting and exploring RNA motif are prone to lie in modeling, engineering, and this is partly why we need computational biology.
RNA structural motifs are the building blocks of the complex RNA architecture. Identification of non-coding RNA structural motifs is a critical step towards understanding of their structures and functionalities. In this article, we present a clustering approach for de novo RNA structural motif identification. We applied our approach on a data set containing 5S, 16S and 23S rRNAs and rediscovered many known motifs including GNRA tetraloop, kink-turn, C-loop, sarcin–ricin, reverse kink-turn, hook-turn, E-loop and tandem-sheared motifs, with higher accuracy than the state-of-the-art clustering method. We also identified a number of potential novel instances of GNRA tetraloop, kink-turn, sarcin–ricin and tandem-sheared motifs. More importantly, several novel structural motif families have been revealed by our clustering analysis. We identified a highly asymmetric bulge loop motif that resembles the rope sling. We also found an internal loop motif that can significantly increase the twist of the helix. Finally, we discovered a subfamily of hexaloop motif, which has significantly different geometry comparing to the currently known hexaloop motif. Our discoveries presented in this article have largely increased current knowledge of RNA structural motifs.
Researchers at University of Central Florida [1] used a complex computer program to analyze RNA motifs — the subunits that make up RNA (ribonucleic acid).
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[1] C. Zhong, S. Zhang. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.Nucleic Acids Research, 2011; 40 (3): 1307 DOI:10.1093/nar/gkr804