RNAMotifScanX: a graph alignment approach for RNA structural motif identification.RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture.  In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm.  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.  The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.
RNAMotifScanX
The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.
GNU C++