Feature-based 3D motif filtering for ribosomal RNA

Abstract

RNA 3D motifs are recurrent substructures in an RNA subunit and are building blocks of the RNA architecture. They play an important role in binding proteins and consolidating RNA tertiary structures. RNA 3D motif searching consists of two steps: candidate generation and candidate filtering. We proposed a novel method, known as Feature-based RNA Motif Filtering (FRMF), for identifying motifs based on a set of moment invariants and the Earth Mover's Distance in the second step. A positive set of RNA motifs belonging to six characteristic types, with eight subtypes occurring in HM 50S, is compiled by us. The proposed method is validated on this representative set. FRMF successfully finds most of the positive fragments. Besides the proposed new method and the compiled positive set, we also recognize some new motifs, in particular a π-turn and some non-standard A-minor motifs are found. These newly discovered motifs provide more information about RNA structure conformation. Matlab code can be downloaded from www.cs.cityu.edu.hk/~yingshen/FRMF.html cshswong@cityu.edu.hk Supplementary data are available at Bioinformatics online.