Poster abstracts
Poster number 74 submitted by James Roll
Identification of 3D motifs in Rfam with JAR3D
James Roll (Department of Computer Science, University of Findlay), Craig Zirbel (Department of Mathematics and Statistics, Bowling Green State University)
Abstract:
Many non-protein-coding RNAs have been discovered and more are being discovered each year. At first we know them only by their sequence, but to understand their function, we need to understand aspects of their 3D structure. Many hairpin and internal loops are known to form structured 3D motifs which are recurrent across different non-coding RNAs, for example, kink turn and sarcin-ricin internal loops, and GNRA hairpin loops. As such, a new non-protein-coding RNA may well have one or more known structured 3D motifs. JAR3D was developed to map sequences of hairpin and internal loops to known 3D motifs, and was recently extended to 3-way and 4-way junction motifs. We applied JAR3D to 4,166 Rfam seed alignments from Rfam 15.0 and made the results accessible on the JAR3D web page, which makes it easy to inspect and evaluate the possible matches for each loop in each Rfam family. We provide several examples which validate JAR3D's ability to identify the correct motif, using 3D structures of RNAs outside of the training set. We created a new page to search for instances of a particular motif across all Rfam families, to facilitate studies of how widespread the occurrence of each motif is. We provide statistics on how many Rfam loops appear to match well to a known 3D motif.
Keywords: non-coding RNA, Rfam, RNA 3D motifs