Title

RNAMotifScanX: a graph alignment approach for RNA structural motif identification

Authors

Authors

RNA-Publ. RNA Soc.

Comments

Authors: contact us about adding a copy of your work at STARS@ucf.edu

Abbreviated Journal Title

Oncogene

Keywords

RNA structural motif; noncanonical base pair; base-stacking interaction; ribosomal RNA; BASE-PAIRS; RIBOSOMAL-RNA; AUTOMATIC IDENTIFICATION; 3-DIMENSIONAL; STRUCTURES; ISOSTERICITY MATRICES; SECONDARY STRUCTURE; PAIRWISE; ALIGNMENT; BUILDING-BLOCKS; NONCODING RNAS; 3D STRUCTURES; Biochemistry & Molecular Biology

Abstract

RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers noncanonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared with other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA.

Subjects

C. C. Zhong;S. J. Zhang

Volume

21

Issue/Number

3

Publication Date

1-1-2014

Document Type

Article

Language

English

First Page

333

Last Page

346

WOS Identifier

WOS:000349848800003

ISSN

1355-8382

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